# Copyright 2009 by Michiel de Hoon. All rights reserved. # Revisions copyright 2010 by Peter Cock. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Test for the SwissProt parser on SwissProt files.""" import os import unittest from Bio import SeqIO from Bio import SwissProt from Bio.SeqRecord import SeqRecord class TestSwissProt(unittest.TestCase): def test_Q13454(self): """Parsing SwissProt file Q13454.txt.""" filename = "Q13454.txt" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "Q13454") self.assertEqual(seq_record.name, "TUSC3_HUMAN") self.assertEqual( seq_record.description, "RecName: Full=Tumor suppressor candidate 3; AltName: Full=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TUSC3; Short=Oligosaccharyl transferase subunit TUSC3; AltName: Full=Magnesium uptake/transporter TUSC3; AltName: Full=Protein N33; Flags: Precursor;", ) self.assertEqual( repr(seq_record.seq), "Seq('MGARGAPSRRRQAGRRLRYLPTGSFPFLLLLLLLCIQLGGGQKKKENLLAEKVE...DFE')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "TUSC3_HUMAN") self.assertEqual( record.accessions, ["Q13454", "A8MSM0", "D3DSP2", "Q14911", "Q14912", "Q96FW0"], ) self.assertEqual(record.gene_name, [{"Name": "TUSC3", "Synonyms": ["N33"]}]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Euarchontoglires", "Primates", "Haplorrhini", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (348, 39676, "16D97CB1E00C5190")) self.assertEqual(len(record.features), 32) feature = record.features[0] self.assertEqual(feature.type, "SIGNAL") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 41) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[1] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 41) self.assertEqual(feature.location.end, 348) self.assertEqual(feature.qualifiers["note"], "Tumor suppressor candidate 3") self.assertEqual(feature.id, "PRO_0000215300") feature = record.features[2] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 41) self.assertEqual(feature.location.end, 196) self.assertEqual(feature.qualifiers["note"], "Lumenal") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[3] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 196) self.assertEqual(feature.location.end, 217) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[4] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 217) self.assertEqual(feature.location.end, 221) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[5] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 221) self.assertEqual(feature.location.end, 242) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[6] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 242) self.assertEqual(feature.location.end, 276) self.assertEqual(feature.qualifiers["note"], "Lumenal") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[7] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 276) self.assertEqual(feature.location.end, 297) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[8] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 297) self.assertEqual(feature.location.end, 312) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[9] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 312) self.assertEqual(feature.location.end, 333) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[10] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 333) self.assertEqual(feature.location.end, 348) self.assertEqual(feature.qualifiers["note"], "Lumenal") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) feature = record.features[11] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 58) self.assertEqual(feature.location.end, 187) self.assertEqual(feature.qualifiers["note"], "Thioredoxin") self.assertIsNone(feature.id) feature = record.features[12] self.assertEqual(feature.type, "DISULFID") self.assertEqual(feature.location.start, 98) self.assertEqual(feature.location.end, 102) self.assertEqual(feature.qualifiers["note"], "Redox-active") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:24685145,ECO:0007744|PDB:4M8G, ECO:0007744|PDB:4M90", ) self.assertIsNone(feature.id) feature = record.features[13] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 343) self.assertEqual(feature.location.end, 348) self.assertEqual(feature.qualifiers["note"], "DLDFE -> FLIK (in isoform 2)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:8661104", ) self.assertEqual(feature.id, "VSP_003776") feature = record.features[14] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 64) self.assertEqual(feature.location.end, 65) self.assertEqual(feature.qualifiers["note"], "I -> V (in dbSNP:rs11545035)") self.assertEqual(feature.id, "VAR_045836") feature = record.features[15] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 246) self.assertEqual(feature.location.end, 247) self.assertEqual(feature.qualifiers["note"], "M -> V") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:23033978") self.assertEqual(feature.id, "VAR_069369") feature = record.features[16] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 98) self.assertEqual(feature.location.end, 99) self.assertEqual( feature.qualifiers["note"], "C->S: Reduces N-glycosylation of cysteine-proximal acceptor sites; when associated with S-102.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:25135935") self.assertIsNone(feature.id) feature = record.features[17] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 101) self.assertEqual(feature.location.end, 102) self.assertEqual( feature.qualifiers["note"], "C->S: Reduces N-glycosylation of cysteine-proximal acceptor sites; when associated with S-99.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:25135935") self.assertIsNone(feature.id) feature = record.features[18] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 43) self.assertEqual(feature.location.end, 62) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[19] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 63) self.assertEqual(feature.location.end, 67) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[20] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 69) self.assertEqual(feature.location.end, 76) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[21] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 83) self.assertEqual(feature.location.end, 91) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[22] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 94) self.assertEqual(feature.location.end, 97) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[23] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 99) self.assertEqual(feature.location.end, 118) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[24] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 125) self.assertEqual(feature.location.end, 132) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[25] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 132) self.assertEqual(feature.location.end, 135) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[26] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 136) self.assertEqual(feature.location.end, 142) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[27] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 149) self.assertEqual(feature.location.end, 154) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[28] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 155) self.assertEqual(feature.location.end, 158) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[29] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 161) self.assertEqual(feature.location.end, 164) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[30] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 167) self.assertEqual(feature.location.end, 171) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) feature = record.features[31] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 174) self.assertEqual(feature.location.end, 186) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4M91") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 12) self.assertEqual( record.references[0].authors, "Macgrogan D., Levy A., Bova G.S., Isaacs W.B., Bookstein R.", ) self.assertEqual( record.references[0].title, "Structure and methylation-associated silencing of a gene within a homozygously deleted region of human chromosome band 8p22.", ) self.assertEqual( record.references[0].positions, ["NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORMS 1 AND 2)."], ) self.assertEqual(len(record.references[0].references), 2) self.assertEqual(record.references[0].references[0], ("PubMed", "8661104")) self.assertEqual( record.references[0].references[1], ("DOI", "10.1006/geno.1996.0322") ) self.assertEqual( record.references[1].authors, "Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.", ) self.assertEqual( record.references[1].title, "Cloning of human full-length CDSs in BD Creator(TM) system donor vector.", ) self.assertEqual( record.references[1].positions, ["NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1)."], ) self.assertEqual(len(record.references[1].references), 0) self.assertEqual( record.references[2].authors, "Nusbaum C., Mikkelsen T.S., Zody M.C., Asakawa S., Taudien S., Garber M., Kodira C.D., Schueler M.G., Shimizu A., Whittaker C.A., Chang J.L., Cuomo C.A., Dewar K., FitzGerald M.G., Yang X., Allen N.R., Anderson S., Asakawa T., Blechschmidt K., Bloom T., Borowsky M.L., Butler J., Cook A., Corum B., DeArellano K., DeCaprio D., Dooley K.T., Dorris L. III, Engels R., Gloeckner G., Hafez N., Hagopian D.S., Hall J.L., Ishikawa S.K., Jaffe D.B., Kamat A., Kudoh J., Lehmann R., Lokitsang T., Macdonald P., Major J.E., Matthews C.D., Mauceli E., Menzel U., Mihalev A.H., Minoshima S., Murayama Y., Naylor J.W., Nicol R., Nguyen C., O'Leary S.B., O'Neill K., Parker S.C.J., Polley A., Raymond C.K., Reichwald K., Rodriguez J., Sasaki T., Schilhabel M., Siddiqui R., Smith C.L., Sneddon T.P., Talamas J.A., Tenzin P., Topham K., Venkataraman V., Wen G., Yamazaki S., Young S.K., Zeng Q., Zimmer A.R., Rosenthal A., Birren B.W., Platzer M., Shimizu N., Lander E.S.", ) self.assertEqual( record.references[2].title, "DNA sequence and analysis of human chromosome 8.", ) self.assertEqual( record.references[2].positions, ["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]."], ) self.assertEqual(len(record.references[2].references), 2) self.assertEqual(record.references[2].references[0], ("PubMed", "16421571")) self.assertEqual( record.references[2].references[1], ("DOI", "10.1038/nature04406") ) self.assertEqual( record.references[3].authors, "Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.", ) self.assertEqual( record.references[3].title, "", ) self.assertEqual( record.references[3].positions, ["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]."], ) self.assertEqual(len(record.references[3].references), 0) self.assertEqual( record.references[4].authors, "The MGC Project Team", ) self.assertEqual( record.references[4].title, "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).", ) self.assertEqual( record.references[4].positions, ["NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2)."], ) self.assertEqual(len(record.references[4].references), 2) self.assertEqual(record.references[4].references[0], ("PubMed", "15489334")) self.assertEqual( record.references[4].references[1], ("DOI", "10.1101/gr.2596504") ) self.assertEqual( record.references[5].authors, "Kelleher D.J., Karaoglu D., Mandon E.C., Gilmore R.", ) self.assertEqual( record.references[5].title, "Oligosaccharyltransferase isoforms that contain different catalytic STT3 subunits have distinct enzymatic properties.", ) self.assertEqual( record.references[5].positions, [ "IDENTIFICATION IN THE OLIGOSACCHARYLTRANSFERASE (OST) COMPLEX, AND TISSUE", "SPECIFICITY.", ], ) self.assertEqual(len(record.references[5].references), 2) self.assertEqual(record.references[5].references[0], ("PubMed", "12887896")) self.assertEqual( record.references[5].references[1], ("DOI", "10.1016/s1097-2765(03)00243-0") ) self.assertEqual( record.references[6].authors, "Molinari F., Foulquier F., Tarpey P.S., Morelle W., Boissel S., Teague J., Edkins S., Futreal P.A., Stratton M.R., Turner G., Matthijs G., Gecz J., Munnich A., Colleaux L.", ) self.assertEqual( record.references[6].title, "Oligosaccharyltransferase-subunit mutations in nonsyndromic mental retardation.", ) self.assertEqual(record.references[6].positions, ["INVOLVEMENT IN MRT7."]) self.assertEqual(len(record.references[6].references), 2) self.assertEqual(record.references[6].references[0], ("PubMed", "18455129")) self.assertEqual( record.references[6].references[1], ("DOI", "10.1016/j.ajhg.2008.03.021") ) self.assertEqual( record.references[7].authors, "Garshasbi M., Hadavi V., Habibi H., Kahrizi K., Kariminejad R., Behjati F., Tzschach A., Najmabadi H., Ropers H.H., Kuss A.W.", ) self.assertEqual( record.references[7].title, "A defect in the TUSC3 gene is associated with autosomal recessive mental retardation.", ) self.assertEqual(record.references[7].positions, ["INVOLVEMENT IN MRT7."]) self.assertEqual(len(record.references[7].references), 2) self.assertEqual(record.references[7].references[0], ("PubMed", "18452889")) self.assertEqual( record.references[7].references[1], ("DOI", "10.1016/j.ajhg.2008.03.018") ) self.assertEqual( record.references[8].authors, "Zhou H., Clapham D.E.", ) self.assertEqual( record.references[8].title, "Mammalian MagT1 and TUSC3 are required for cellular magnesium uptake and vertebrate embryonic development.", ) self.assertEqual( record.references[8].positions, ["FUNCTION IN MAGNESIUM UPTAKE."] ) self.assertEqual(len(record.references[8].references), 2) self.assertEqual(record.references[8].references[0], ("PubMed", "19717468")) self.assertEqual( record.references[8].references[1], ("DOI", "10.1073/pnas.0908332106") ) self.assertEqual( record.references[9].authors, "Cherepanova N.A., Shrimal S., Gilmore R.", ) self.assertEqual( record.references[9].title, "Oxidoreductase activity is necessary for N-glycosylation of cysteine-proximal acceptor sites in glycoproteins.", ) self.assertEqual( record.references[9].positions, ["FUNCTION, AND MUTAGENESIS OF CYS-99 AND CYS-102."], ) self.assertEqual(len(record.references[9].references), 2) self.assertEqual(record.references[9].references[0], ("PubMed", "25135935")) self.assertEqual( record.references[9].references[1], ("DOI", "10.1083/jcb.201404083") ) self.assertEqual( record.references[10].authors, "Mohorko E., Owen R.L., Malojcic G., Brozzo M.S., Aebi M., Glockshuber R.", ) self.assertEqual( record.references[10].title, "Structural basis of substrate specificity of human oligosaccharyl transferase subunit N33/Tusc3 and its role in regulating protein N-glycosylation.", ) self.assertEqual( record.references[10].positions, [ "X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) OF 44-194, DISULFIDE BOND, PROPOSED", "FUNCTION, AND SUBUNIT.", ], ) self.assertEqual(len(record.references[10].references), 2) self.assertEqual(record.references[10].references[0], ("PubMed", "24685145")) self.assertEqual( record.references[10].references[1], ("DOI", "10.1016/j.str.2014.02.013") ) self.assertEqual( record.references[11].authors, "de Ligt J., Willemsen M.H., van Bon B.W., Kleefstra T., Yntema H.G., Kroes T., Vulto-van Silfhout A.T., Koolen D.A., de Vries P., Gilissen C., del Rosario M., Hoischen A., Scheffer H., de Vries B.B., Brunner H.G., Veltman J.A., Vissers L.E.", ) self.assertEqual( record.references[11].title, "Diagnostic exome sequencing in persons with severe intellectual disability.", ) self.assertEqual(record.references[11].positions, ["VARIANT VAL-247."]) self.assertEqual(len(record.references[11].references), 2) self.assertEqual(record.references[11].references[0], ("PubMed", "23033978")) self.assertEqual( record.references[11].references[1], ("DOI", "10.1056/nejmoa1206524") ) # Check that the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_P60904(self): """Parsing SwissProt file P60904.txt.""" filename = "P60904.txt" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "P60904") self.assertEqual(seq_record.name, "DNJC5_MOUSE") self.assertEqual( seq_record.description, "RecName: Full=DnaJ homolog subfamily C member 5 {ECO:0000305}; AltName: Full=Cysteine string protein {ECO:0000250|UniProtKB:Q9H3Z4}; Short=CSP {ECO:0000250|UniProtKB:Q9H3Z4}; AltName: Full=Cysteine-string protein isoform alpha {ECO:0000303|PubMed:20847230};", ) self.assertEqual( repr(seq_record.seq), "Seq('MADQRQRSLSTSGESLYHVLGLDKNATSDDIKKSYRKLALKYHPDKNPDNPEAA...GFN')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "DNJC5_MOUSE") self.assertEqual(record.accessions, ["P60904", "P54101"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Euarchontoglires", "Glires", "Rodentia", "Myomorpha", "Muroidea", "Muridae", "Murinae", "Mus", "Mus", ], ) self.assertEqual(record.seqinfo, (198, 22101, "52F98261FBAD978F")) self.assertEqual(len(record.features), 23) feature = record.features[0] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 198) self.assertEqual( feature.qualifiers["note"], "DnaJ homolog subfamily C member 5" ) feature = record.features[1] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 12) self.assertEqual(feature.location.end, 82) self.assertEqual(feature.qualifiers["note"], "J") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|PROSITE-ProRule:PRU00286" ) feature = record.features[2] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 7) self.assertEqual(feature.location.end, 8) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250|UniProtKB:Q9H3Z4") feature = record.features[3] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 9) self.assertEqual(feature.location.end, 10) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0007744|PubMed:19131326") feature = record.features[4] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 11) self.assertEqual(feature.location.end, 12) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250|UniProtKB:Q9H3Z4") feature = record.features[5] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 14) self.assertEqual(feature.location.end, 15) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0007744|PubMed:21183079") feature = record.features[6] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 16) self.assertEqual(feature.location.end, 17) self.assertEqual(feature.qualifiers["note"], "Phosphotyrosine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250|UniProtKB:Q9H3Z4") feature = record.features[7] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 55) self.assertEqual(feature.location.end, 56) self.assertEqual(feature.qualifiers["note"], "N6-acetyllysine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250|UniProtKB:Q9H3Z4") feature = record.features[8] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 150) self.assertEqual(feature.location.end, 151) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0007744|PubMed:21183079") feature = record.features[9] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 9) self.assertEqual(feature.location.end, 10) self.assertEqual( feature.qualifiers["note"], "S->D: Reduced interaction with SYT9, but no effect on the interaction with HSC70.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:20847230") feature = record.features[10] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 92) self.assertEqual(feature.location.end, 93) self.assertEqual( feature.qualifiers["note"], "E->V: Reduced interaction with SYT9." ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:20847230") feature = record.features[11] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 112) self.assertEqual(feature.location.end, 113) self.assertEqual( feature.qualifiers["note"], "C->V: No effect on palmitoylation. No change in subcellular location; when associated with G-118 and F-121.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:17034881") feature = record.features[12] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 117) self.assertEqual(feature.location.end, 118) self.assertEqual( feature.qualifiers["note"], "C->G: No effect on palmitoylation. No change in subcellular location; when associated with V-113 and F-121.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:17034881") feature = record.features[13] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 120) self.assertEqual(feature.location.end, 121) self.assertEqual( feature.qualifiers["note"], "C->F: No effect on palmitoylation. No change in subcellular location; when associated with V-113 and G-118.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:17034881") feature = record.features[14] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 128) self.assertEqual(feature.location.end, 129) self.assertEqual( feature.qualifiers["note"], "F->C: No effect on palmitoylation. No change in subcellular location; when associated with H-135.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:17034881") feature = record.features[15] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 134) self.assertEqual(feature.location.end, 135) self.assertEqual( feature.qualifiers["note"], "K->H: No effect on palmitoylation. No change in subcellular location; when associated with C-129.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:17034881") feature = record.features[16] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 15) self.assertEqual(feature.location.end, 20) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:2CTW") feature = record.features[17] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 27) self.assertEqual(feature.location.end, 41) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:2CTW") feature = record.features[18] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 43) self.assertEqual(feature.location.end, 46) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:2CTW") feature = record.features[19] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 50) self.assertEqual(feature.location.end, 67) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:2CTW") feature = record.features[20] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 69) self.assertEqual(feature.location.end, 78) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:2CTW") feature = record.features[21] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 80) self.assertEqual(feature.location.end, 89) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:2CTW") feature = record.features[22] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 93) self.assertEqual(feature.location.end, 100) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:2CTW") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 16) reference = record.references[0] self.assertEqual(reference.authors, "Qin N., Lin T., Birnbaumer L.") self.assertEqual(reference.title, "") self.assertEqual(len(reference.references), 0) reference = record.references[1] self.assertEqual( reference.authors, "Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J., Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.", ) self.assertEqual( reference.title, "The transcriptional landscape of the mammalian genome." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "16141072")) self.assertEqual(reference.references[1], ("DOI", "10.1126/science.1112014")) reference = record.references[2] self.assertEqual(reference.authors, "Lubec G., Kang S.U.") self.assertEqual(reference.title, "") self.assertEqual(len(reference.references), 0) reference = record.references[3] self.assertEqual( reference.authors, "Boal F., Le Pevelen S., Cziepluch C., Scotti P., Lang J.", ) self.assertEqual( reference.title, "Cysteine-string protein isoform beta (Cspbeta) is targeted to the trans-Golgi network as a non-palmitoylated CSP in clonal beta-cells.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17034881")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.bbamcr.2006.08.054") ) reference = record.references[4] self.assertEqual( reference.authors, "Lee J., Xu Y., Chen Y., Sprung R., Kim S.C., Xie S., Zhao Y.", ) self.assertEqual( reference.title, "Mitochondrial phosphoproteome revealed by an improved IMAC method and MS/MS/MS.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17208939")) self.assertEqual(reference.references[1], ("DOI", "10.1074/mcp.m600218-mcp200")) reference = record.references[5] self.assertEqual( reference.authors, "Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P." ) self.assertEqual( reference.title, "Large-scale phosphorylation analysis of mouse liver." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17242355")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.0609836104")) reference = record.references[6] self.assertEqual( reference.authors, "Zhou H., Ye M., Dong J., Han G., Jiang X., Wu R., Zou H.", ) self.assertEqual( reference.title, "Specific phosphopeptide enrichment with immobilized titanium ion affinity chromatography adsorbent for phosphoproteome analysis.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "18630941")) self.assertEqual(reference.references[1], ("DOI", "10.1021/pr800223m")) reference = record.references[7] self.assertEqual( reference.authors, "Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.", ) self.assertEqual( reference.title, "The phagosomal proteome in interferon-gamma-activated macrophages.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19144319")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.immuni.2008.11.006") ) reference = record.references[8] self.assertEqual( reference.authors, "Sweet S.M., Bailey C.M., Cunningham D.L., Heath J.K., Cooper H.J.", ) self.assertEqual( reference.title, "Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19131326")) self.assertEqual(reference.references[1], ("DOI", "10.1074/mcp.m800451-mcp200")) reference = record.references[9] self.assertEqual( reference.authors, "Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R., Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.", ) self.assertEqual( reference.title, "A tissue-specific atlas of mouse protein phosphorylation and expression.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21183079")) self.assertEqual(reference.references[1], ("DOI", "10.1016/j.cell.2010.12.001")) reference = record.references[10] self.assertEqual( reference.authors, "Boal F., Laguerre M., Milochau A., Lang J., Scotti P.A." ) self.assertEqual( reference.title, "A charged prominence in the linker domain of the cysteine-string protein Cspalpha mediates its regulated interaction with the calcium sensor synaptotagmin 9 during exocytosis.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "20847230")) self.assertEqual(reference.references[1], ("DOI", "10.1096/fj.09-152033")) reference = record.references[11] self.assertEqual( reference.authors, "Sharma M., Burre J., Bronk P., Zhang Y., Xu W., Suedhof T.C.", ) self.assertEqual( reference.title, "CSPalpha knockout causes neurodegeneration by impairing SNAP-25 function.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "22187053")) self.assertEqual(reference.references[1], ("DOI", "10.1038/emboj.2011.467")) reference = record.references[12] self.assertEqual( reference.authors, "Lemonidis K., Gorleku O.A., Sanchez-Perez M.C., Grefen C., Chamberlain L.H.", ) self.assertEqual( reference.title, "The Golgi S-acylation machinery comprises zDHHC enzymes with major differences in substrate affinity and S-acylation activity.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "25253725")) self.assertEqual(reference.references[1], ("DOI", "10.1091/mbc.e14-06-1169")) reference = record.references[13] self.assertEqual( reference.authors, "Lemonidis K., Sanchez-Perez M.C., Chamberlain L.H." ) self.assertEqual( reference.title, "Identification of a novel sequence motif recognized by the ankyrin repeat domain of zDHHC17/13 S-acyltransferases.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "26198635")) self.assertEqual(reference.references[1], ("DOI", "10.1074/jbc.m115.657668")) reference = record.references[14] self.assertEqual(reference.authors, "Burgoyne R.D., Morgan A.") self.assertEqual( reference.title, "Cysteine string protein (CSP) and its role in preventing neurodegeneration.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "25800794")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.semcdb.2015.03.008") ) reference = record.references[15] self.assertEqual( reference.authors, "RIKEN structural genomics initiative (RSGI)" ) self.assertEqual( reference.title, "Solution structure of J-domain from mouse DnaJ subfamily C member 5.", ) self.assertEqual(len(reference.references), 0) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_P62258(self): """Parsing SwissProt file P62258.""" filename = "P62258.txt" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "P62258") self.assertEqual(seq_record.name, "1433E_HUMAN") self.assertEqual( seq_record.description, "RecName: Full=14-3-3 protein epsilon; Short=14-3-3E;", ) self.assertEqual( repr(seq_record.seq), "Seq('MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIG...ENQ')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "1433E_HUMAN") self.assertEqual( record.accessions, [ "P62258", "B3KY71", "D3DTH5", "P29360", "P42655", "Q4VJB6", "Q53XZ5", "Q63631", "Q7M4R4", ], ) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Euarchontoglires", "Primates", "Haplorrhini", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (255, 29174, "07817CCBD1F75B26")) self.assertEqual(len(record.features), 32) self.assertEqual(len(record.references), 46) reference = record.references[0] self.assertEqual(reference.authors, "Conklin D.S., Galaktionov K., Beach D.") self.assertEqual( reference.title, "14-3-3 proteins associate with cdc25 phosphatases." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "7644510")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.92.17.7892")) reference = record.references[1] self.assertEqual( reference.authors, "Chong S.S., Tanigami A., Roschke A.V., Ledbetter D.H." ) self.assertEqual( reference.title, "14-3-3 epsilon has no homology to LIS1 and lies telomeric to it on chromosome 17p13.3 outside the Miller-Dieker syndrome chromosome region.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8858348")) self.assertEqual(reference.references[1], ("DOI", "10.1101/gr.6.8.735")) reference = record.references[2] self.assertEqual( reference.authors, "Jin D.-Y., Lyu M.S., Kozak C.A., Jeang K.-T." ) self.assertEqual(reference.title, "Function of 14-3-3 proteins.") self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8684458")) self.assertEqual(reference.references[1], ("DOI", "10.1038/382308a0")) reference = record.references[3] self.assertEqual( reference.authors, "Han D., Ye G., Liu T., Chen C., Yang X., Wan B., Pan Y., Yu L.", ) self.assertEqual( reference.title, "Functional identification of a novel 14-3-3 epsilon splicing variant suggests dimerization is not necessary for 14-3-3 epsilon to inhibit UV-induced apoptosis.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "20417184")) self.assertEqual(reference.references[1], ("DOI", "10.1016/j.bbrc.2010.04.104")) reference = record.references[4] self.assertEqual(reference.authors, "Luk S.C.W., Lee C.Y., Waye M.M.Y.") self.assertEqual( reference.title, "Sequence determination of human epsilon 14-3-3 protein." ) self.assertEqual(len(reference.references), 0) reference = record.references[5] self.assertEqual(reference.authors, "Tanigami A., Chong S.S., Ledbetter D.H.") self.assertEqual(reference.title, "14-3-3 epsilon genomic sequence.") self.assertEqual(len(reference.references), 0) reference = record.references[6] self.assertEqual( reference.authors, "Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S., Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.", ) self.assertEqual( reference.title, "Complete sequencing and characterization of 21,243 full-length human cDNAs.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "14702039")) self.assertEqual(reference.references[1], ("DOI", "10.1038/ng1285")) reference = record.references[7] self.assertEqual( reference.authors, "Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.", ) self.assertEqual( reference.title, "Cloning of human full-length CDSs in BD Creator(TM) system donor vector.", ) self.assertEqual(len(reference.references), 0) reference = record.references[8] self.assertEqual( reference.authors, "Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.", ) self.assertEqual(reference.title, "") self.assertEqual(len(reference.references), 0) reference = record.references[9] self.assertEqual(reference.authors, "The MGC Project Team") self.assertEqual( reference.title, "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "15489334")) self.assertEqual(reference.references[1], ("DOI", "10.1101/gr.2596504")) reference = record.references[10] self.assertEqual( reference.authors, "Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., Vandekerckhove J.", ) self.assertEqual( reference.title, "Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "12665801")) self.assertEqual(reference.references[1], ("DOI", "10.1038/nbt810")) reference = record.references[11] self.assertEqual( reference.authors, "Greninger A.L., Knudsen G.M., Betegon M., Burlingame A.L., DeRisi J.L.", ) self.assertEqual( reference.title, "ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "23572552")) self.assertEqual(reference.references[1], ("DOI", "10.1128/mbio.00098-13")) reference = record.references[12] self.assertEqual(reference.authors, "Bienvenut W.V.") self.assertEqual(reference.title, "") self.assertEqual(len(reference.references), 0) reference = record.references[13] self.assertEqual( reference.authors, "Stewart S., Sundaram M., Zhang Y., Lee J., Han M., Guan K.L.", ) self.assertEqual( reference.title, "Kinase suppressor of Ras forms a multiprotein signaling complex and modulates MEK localization.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "10409742")) self.assertEqual(reference.references[1], ("DOI", "10.1128/mcb.19.8.5523")) reference = record.references[14] self.assertEqual( reference.authors, "Demeter J., Medzihradszky D., Kha H., Goetzl E.J., Turck C.W.", ) self.assertEqual( reference.title, "Isolation and partial characterization of the structures of fibroblast activating factor-related proteins from U937 cells.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "2026444")) reference = record.references[15] self.assertEqual(reference.authors, "Lubec G., Afjehi-Sadat L.") self.assertEqual(reference.title, "") self.assertEqual(len(reference.references), 0) reference = record.references[16] self.assertEqual( reference.authors, "Aoki H., Hayashi J., Moriyama M., Arakawa Y., Hino O." ) self.assertEqual( reference.title, "Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "10644344")) self.assertEqual( reference.references[1], ("DOI", "10.1128/jvi.74.4.1736-1741.2000") ) reference = record.references[17] self.assertEqual( reference.authors, "Ganguly S., Gastel J.A., Weller J.L., Schwartz C., Jaffe H., Namboodiri M.A., Coon S.L., Hickman A.B., Rollag M., Obsil T., Beauverger P., Ferry G., Boutin J.A., Klein D.C.", ) self.assertEqual( reference.title, "Role of a pineal cAMP-operated arylalkylamine N-acetyltransferase/14-3-3-binding switch in melatonin synthesis.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "11427721")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.141118798")) reference = record.references[18] self.assertEqual( reference.authors, "Fujita N., Sato S., Katayama K., Tsuruo T." ) self.assertEqual( reference.title, "Akt-dependent phosphorylation of p27Kip1 promotes binding to 14-3-3 and cytoplasmic localization.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "12042314")) self.assertEqual(reference.references[1], ("DOI", "10.1074/jbc.m203668200")) reference = record.references[19] self.assertEqual( reference.authors, "Wang X., Grammatikakis N., Siganou A., Calderwood S.K." ) self.assertEqual( reference.title, "Regulation of molecular chaperone gene transcription involves the serine phosphorylation, 14-3-3 epsilon binding, and cytoplasmic sequestration of heat shock factor 1.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "12917326")) self.assertEqual( reference.references[1], ("DOI", "10.1128/mcb.23.17.6013-6026.2003") ) reference = record.references[20] self.assertEqual( reference.authors, "Andersen J.S., Wilkinson C.J., Mayor T., Mortensen P., Nigg E.A., Mann M.", ) self.assertEqual( reference.title, "Proteomic characterization of the human centrosome by protein correlation profiling.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "14654843")) self.assertEqual(reference.references[1], ("DOI", "10.1038/nature02166")) reference = record.references[21] self.assertEqual( reference.authors, "Urschel S., Bassermann F., Bai R.Y., Munch S., Peschel C., Duyster J.", ) self.assertEqual( reference.title, "Phosphorylation of grb10 regulates its interaction with 14-3-3.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "15722337")) self.assertEqual(reference.references[1], ("DOI", "10.1074/jbc.m501477200")) reference = record.references[22] self.assertEqual( reference.authors, "Yoshida K., Yamaguchi T., Natsume T., Kufe D., Miki Y." ) self.assertEqual( reference.title, "JNK phosphorylation of 14-3-3 proteins regulates nuclear targeting of c-Abl in the apoptotic response to DNA damage.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "15696159")) self.assertEqual(reference.references[1], ("DOI", "10.1038/ncb1228")) reference = record.references[23] self.assertEqual( reference.authors, "Gu Y.-M., Jin Y.-H., Choi J.-K., Baek K.-H., Yeo C.-Y., Lee K.-Y.", ) self.assertEqual( reference.title, "Protein kinase A phosphorylates and regulates dimerization of 14-3-3 epsilon.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "16376338")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.febslet.2005.12.024") ) reference = record.references[24] self.assertEqual( reference.authors, "Chi A., Valencia J.C., Hu Z.-Z., Watabe H., Yamaguchi H., Mangini N.J., Huang H., Canfield V.A., Cheng K.C., Yang F., Abe R., Yamagishi S., Shabanowitz J., Hearing V.J., Wu C., Appella E., Hunt D.F.", ) self.assertEqual( reference.title, "Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17081065")) self.assertEqual(reference.references[1], ("DOI", "10.1021/pr060363j")) reference = record.references[25] self.assertEqual( reference.authors, "Linde C.I., Di Leva F., Domi T., Tosatto S.C., Brini M., Carafoli E.", ) self.assertEqual( reference.title, "Inhibitory interaction of the 14-3-3 proteins with ubiquitous (PMCA1) and tissue-specific (PMCA3) isoforms of the plasma membrane Ca2+ pump.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "18029012")) self.assertEqual(reference.references[1], ("DOI", "10.1016/j.ceca.2007.09.003")) reference = record.references[26] self.assertEqual( reference.authors, "Brummer T., Larance M., Herrera Abreu M.T., Lyons R.J., Timpson P., Emmerich C.H., Fleuren E.D.G., Lehrbach G.M., Schramek D., Guilhaus M., James D.E., Daly R.J.", ) self.assertEqual( reference.title, "Phosphorylation-dependent binding of 14-3-3 terminates signalling by the Gab2 docking protein.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19172738")) self.assertEqual(reference.references[1], ("DOI", "10.1038/emboj.2008.159")) reference = record.references[27] self.assertEqual( reference.authors, "Han G., Ye M., Zhou H., Jiang X., Feng S., Jiang X., Tian R., Wan D., Zou H., Gu J.", ) self.assertEqual( reference.title, "Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "18318008")) self.assertEqual(reference.references[1], ("DOI", "10.1002/pmic.200700884")) reference = record.references[28] self.assertEqual( reference.authors, "Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.", ) self.assertEqual( reference.title, "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19413330")) self.assertEqual(reference.references[1], ("DOI", "10.1021/ac9004309")) reference = record.references[29] self.assertEqual(reference.authors, "Kajiwara Y., Buxbaum J.D., Grice D.E.") self.assertEqual( reference.title, "SLITRK1 binds 14-3-3 and regulates neurite outgrowth in a phosphorylation-dependent manner.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19640509")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.biopsych.2009.05.033") ) reference = record.references[30] self.assertEqual( reference.authors, "Jang S.W., Liu X., Fu H., Rees H., Yepes M., Levey A., Ye K.", ) self.assertEqual( reference.title, "Interaction of Akt-phosphorylated SRPK2 with 14-3-3 mediates cell cycle and cell death in neurons.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19592491")) self.assertEqual(reference.references[1], ("DOI", "10.1074/jbc.m109.026237")) reference = record.references[31] self.assertEqual( reference.authors, "Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.", ) self.assertEqual( reference.title, "Lysine acetylation targets protein complexes and co-regulates major cellular functions.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19608861")) self.assertEqual(reference.references[1], ("DOI", "10.1126/science.1175371")) reference = record.references[32] self.assertEqual( reference.authors, "Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.", ) self.assertEqual( reference.title, "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "20068231")) self.assertEqual(reference.references[1], ("DOI", "10.1126/scisignal.2000475")) reference = record.references[33] self.assertEqual( reference.authors, "Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.", ) self.assertEqual( reference.title, "Initial characterization of the human central proteome." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21269460")) self.assertEqual(reference.references[1], ("DOI", "10.1186/1752-0509-5-17")) reference = record.references[34] self.assertEqual( reference.authors, "Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.", ) self.assertEqual( reference.title, "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21406692")) self.assertEqual(reference.references[1], ("DOI", "10.1126/scisignal.2001570")) reference = record.references[35] self.assertEqual( reference.authors, "Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J., Mohammed S.", ) self.assertEqual( reference.title, "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "23186163")) self.assertEqual(reference.references[1], ("DOI", "10.1021/pr300630k")) reference = record.references[36] self.assertEqual( reference.authors, "Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.", ) self.assertEqual( reference.title, "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "24275569")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.jprot.2013.11.014") ) reference = record.references[37] self.assertEqual( reference.authors, "Yuasa K., Ota R., Matsuda S., Isshiki K., Inoue M., Tsuji A.", ) self.assertEqual( reference.title, "Suppression of death-associated protein kinase 2 by interaction with 14-3-3 proteins.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "26047703")) self.assertEqual(reference.references[1], ("DOI", "10.1016/j.bbrc.2015.05.105")) reference = record.references[38] self.assertEqual( reference.authors, "Kulasekaran G., Nossova N., Marat A.L., Lund I., Cremer C., Ioannou M.S., McPherson P.S.", ) self.assertEqual( reference.title, "Phosphorylation-dependent regulation of Connecdenn/DENND1 guanine nucleotide exchange factors.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "26055712")) self.assertEqual(reference.references[1], ("DOI", "10.1074/jbc.m115.636712")) reference = record.references[39] self.assertEqual( reference.authors, "Gao K., Tang W., Li Y., Zhang P., Wang D., Yu L., Wang C., Wu D.", ) self.assertEqual( reference.title, "Front-signal-dependent accumulation of the RHOA inhibitor FAM65B at leading edges polarizes neutrophils.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "25588844")) self.assertEqual(reference.references[1], ("DOI", "10.1242/jcs.161497")) reference = record.references[40] self.assertEqual( reference.authors, "Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D., Lane L., Bairoch A., Van Dorsselaer A., Carapito C.", ) self.assertEqual( reference.title, "N-terminome analysis of the human mitochondrial proteome." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "25944712")) self.assertEqual(reference.references[1], ("DOI", "10.1002/pmic.201400617")) reference = record.references[41] self.assertEqual( reference.authors, "Masters S.L., Lagou V., Jeru I., Baker P.J., Van Eyck L., Parry D.A., Lawless D., De Nardo D., Garcia-Perez J.E., Dagley L.F., Holley C.L., Dooley J., Moghaddas F., Pasciuto E., Jeandel P.Y., Sciot R., Lyras D., Webb A.I., Nicholson S.E., De Somer L., van Nieuwenhove E., Ruuth-Praz J., Copin B., Cochet E., Medlej-Hashim M., Megarbane A., Schroder K., Savic S., Goris A., Amselem S., Wouters C., Liston A.", ) self.assertEqual( reference.title, "Familial autoinflammation with neutrophilic dermatosis reveals a regulatory mechanism of pyrin activation.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "27030597")) self.assertEqual( reference.references[1], ("DOI", "10.1126/scitranslmed.aaf1471") ) reference = record.references[42] self.assertEqual( reference.authors, "Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C., Nielsen M.L.", ) self.assertEqual( reference.title, "Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "28112733")) self.assertEqual(reference.references[1], ("DOI", "10.1038/nsmb.3366")) reference = record.references[43] self.assertEqual( reference.authors, "Sonntag T., Ostojic J., Vaughan J.M., Moresco J.J., Yoon Y.S., Yates J.R. III, Montminy M.", ) self.assertEqual( reference.title, "Mitogenic Signals Stimulate the CREB Coactivator CRTC3 through PP2A Recruitment.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "30611118")) self.assertEqual(reference.references[1], ("DOI", "10.1016/j.isci.2018.12.012")) reference = record.references[44] self.assertEqual( reference.authors, "Chen J., Ou Y., Yang Y., Li W., Xu Y., Xie Y., Liu Y." ) self.assertEqual( reference.title, "KLHL22 activates amino-acid-dependent mTORC1 signalling to promote tumorigenesis and ageing.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "29769719")) self.assertEqual(reference.references[1], ("DOI", "10.1038/s41586-018-0128-9")) reference = record.references[45] self.assertEqual( reference.authors, "Yang X., Lee W.H., Sobott F., Papagrigoriou E., Robinson C.V., Grossmann J.G., Sundstroem M., Doyle D.A., Elkins J.M.", ) self.assertEqual( reference.title, "Structural basis for protein-protein interactions in the 14-3-3 protein family.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17085597")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.0605779103")) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_P0A186(self): """Parsing SwissProt file P0A186.txt.""" filename = "P0A186.txt" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "P0A186") self.assertEqual(seq_record.name, "NDOA_PSEU8") self.assertEqual( seq_record.description, "RecName: Full=Naphthalene 1,2-dioxygenase system, ferredoxin component {ECO:0000303|PubMed:8226631};", ) self.assertEqual( repr(seq_record.seq), "Seq('MTVKWIEAVALSDILEGDVLGVTVEGKELALYEVEGEIYATDNLCTHGSARMSD...DLS')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "NDOA_PSEU8") self.assertEqual(record.accessions, ["P0A186", "O07829", "P23082", "Q52123"]) self.assertEqual(record.organism_classification, ["Bacteria", "Proteobacteria"]) self.assertEqual(record.seqinfo, (104, 11446, "475625DCC3EDCD41")) self.assertEqual(len(record.features), 7) feature = record.features[0] self.assertEqual(feature.type, "INIT_MET") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 1) self.assertEqual(feature.qualifiers["note"], "Removed") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250|UniProtKB:P0A185") feature = record.features[1] self.assertEqual(feature.id, "PRO_0000201694") self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 1) self.assertEqual(feature.location.end, 104) self.assertEqual( feature.qualifiers["note"], "Naphthalene 1,2-dioxygenase system, ferredoxin component", ) feature = record.features[2] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 5) self.assertEqual(feature.location.end, 101) self.assertEqual(feature.qualifiers["note"], "Rieske") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|PROSITE-ProRule:PRU00628" ) feature = record.features[3] self.assertEqual(feature.type, "METAL") self.assertEqual(feature.location.start, 44) self.assertEqual(feature.location.end, 45) self.assertEqual(feature.qualifiers["note"], "Iron-sulfur (2Fe-2S)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000250|UniProtKB:P0A185,ECO:0000255|PROSITE-ProRule:PRU00628", ) self.assertIsNone(feature.id) feature = record.features[4] self.assertEqual(feature.type, "METAL") self.assertEqual(feature.location.start, 46) self.assertEqual(feature.location.end, 47) self.assertEqual( feature.qualifiers["note"], "Iron-sulfur (2Fe-2S); via pros nitrogen" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000250|UniProtKB:P0A185,ECO:0000255|PROSITE-ProRule:PRU00628", ) self.assertIsNone(feature.id) feature = record.features[5] self.assertEqual(feature.type, "METAL") self.assertEqual(feature.location.start, 63) self.assertEqual(feature.location.end, 64) self.assertEqual(feature.qualifiers["note"], "Iron-sulfur (2Fe-2S)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000250|UniProtKB:P0A185,ECO:0000255|PROSITE-ProRule:PRU00628", ) self.assertIsNone(feature.id) feature = record.features[6] self.assertEqual(feature.type, "METAL") self.assertEqual(feature.location.start, 66) self.assertEqual(feature.location.end, 67) self.assertEqual( feature.qualifiers["note"], "Iron-sulfur (2Fe-2S); via pros nitrogen" ) self.assertIsNone(feature.id) self.assertEqual(len(record.references), 1) self.assertEqual( record.references[0].authors, "Denome S.A., Stanley D.C., Olson E.S., Young K.D.", ) self.assertEqual( record.references[0].title, "Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of an upper naphthalene catabolic pathway.", ) self.assertEqual(len(record.references[0].references), 2) self.assertEqual(record.references[0].references[0], ("PubMed", "8226631")) self.assertEqual( record.references[0].references[1], ("DOI", "10.1128/jb.175.21.6890-6901.1993"), ) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_P68308(self): """Parsing SwissProt file P68308.txt.""" filename = "P68308.txt" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "P68308") self.assertEqual(seq_record.name, "NU3M_BALPH") self.assertEqual( seq_record.description, "RecName: Full=NADH-ubiquinone oxidoreductase chain 3 {ECO:0000250|UniProtKB:P03897}; EC=7.1.1.2 {ECO:0000250|UniProtKB:P03897}; AltName: Full=NADH dehydrogenase subunit 3;", ) self.assertEqual( repr(seq_record.seq), "Seq('MNLLLTLLTNTTLALLLVFIAFWLPQLNVYAEKTSPYECGFDPMGSARLPFSMK...WAE')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "NU3M_BALPH") self.assertEqual(record.accessions, ["P68308", "P24973"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Laurasiatheria", "Artiodactyla", "Whippomorpha", "Cetacea", "Mysticeti", "Balaenopteridae", "Balaenoptera", ], ) self.assertEqual(record.seqinfo, (115, 13022, "405197D2F5D0AC4B")) self.assertEqual(len(record.features), 4) feature = record.features[0] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 115) self.assertEqual( feature.qualifiers["note"], "NADH-ubiquinone oxidoreductase chain 3" ) feature = record.features[1] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 2) self.assertEqual(feature.location.end, 23) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[2] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 54) self.assertEqual(feature.location.end, 75) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[3] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 83) self.assertEqual(feature.location.end, 104) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 1) reference = record.references[0] self.assertEqual(reference.authors, "Arnason U., Gullberg A., Widegren B.") self.assertEqual( reference.title, "The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1779436")) self.assertEqual(reference.references[1], ("DOI", "10.1007/bf02102808")) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_P39896(self): """Parsing SwissProt file P39896.txt.""" filename = "P39896.txt" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "P39896") self.assertEqual(seq_record.name, "TCMO_STRGA") self.assertEqual( seq_record.description, "RecName: Full=Tetracenomycin polyketide synthesis 8-O-methyl transferase TcmO; EC=2.1.1.-;", ) self.assertEqual( repr(seq_record.seq), "Seq('MTPHTHVRGPGDILQLTMAFYGSRALISAVELDLFTLLAGKPLPLGELCERAGI...KPR')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "TCMO_STRGA") self.assertEqual(record.accessions, ["P39896"]) self.assertEqual( record.organism_classification, [ "Bacteria", "Actinobacteria", "Streptomycetales", "Streptomycetaceae", "Streptomyces", ], ) self.assertEqual(record.seqinfo, (339, 37035, "B228B66B24217F80")) self.assertEqual(len(record.features), 4) feature = record.features[0] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 339) self.assertEqual( feature.qualifiers["note"], "Tetracenomycin polyketide synthesis 8-O-methyl transferase TcmO", ) feature = record.features[1] self.assertEqual(feature.type, "ACT_SITE") self.assertEqual(feature.location.start, 245) self.assertEqual(feature.location.end, 246) self.assertEqual(feature.qualifiers["note"], "Proton acceptor") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|PROSITE-ProRule:PRU01020" ) feature = record.features[2] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 199) self.assertEqual(feature.location.end, 200) self.assertEqual(feature.qualifiers["ligand"], "S-adenosyl-L-methionine") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:59789") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|PROSITE-ProRule:PRU01020" ) feature = record.features[3] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 225) self.assertEqual(feature.location.end, 228) self.assertEqual(feature.qualifiers["ligand"], "S-adenosyl-L-methionine") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:59789") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|PROSITE-ProRule:PRU01020" ) self.assertIsNone(feature.id) self.assertEqual(len(record.references), 1) reference = record.references[0] self.assertEqual( reference.authors, "Summers R.G., Wendt-Pienkowski E., Motamedi H., Hutchinson C.R.", ) self.assertEqual( reference.title, "Nucleotide sequence of the tcmII-tcmIV region of the tetracenomycin C biosynthetic gene cluster of Streptomyces glaucescens and evidence that the tcmN gene encodes a multifunctional cyclase-dehydratase-O-methyl transferase.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1548230")) self.assertEqual( reference.references[1], ("DOI", "10.1128/jb.174.6.1810-1820.1992") ) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_O95832(self): """Parsing SwissProt file O95832.txt.""" filename = "O95832.txt" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "O95832") self.assertEqual(seq_record.name, "CLD1_HUMAN") self.assertEqual( seq_record.description, "RecName: Full=Claudin-1; AltName: Full=Senescence-associated epithelial membrane protein;", ) self.assertEqual( repr(seq_record.seq), "Seq('MANAGLQLLGFILAFLGWIGAIVSTALPQWRIYSYAGDNIVTAQAMYEGLWMSC...DYV')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "CLD1_HUMAN") self.assertEqual(record.accessions, ["O95832"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Euarchontoglires", "Primates", "Haplorrhini", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (211, 22744, "07269000E6C214F0")) self.assertEqual(len(record.features), 17) feature = record.features[0] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 211) self.assertEqual(feature.qualifiers["note"], "Claudin-1") feature = record.features[1] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 7) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250") feature = record.features[2] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 7) self.assertEqual(feature.location.end, 28) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[3] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 28) self.assertEqual(feature.location.end, 81) self.assertEqual(feature.qualifiers["note"], "Extracellular") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[4] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 81) self.assertEqual(feature.location.end, 102) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[5] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 102) self.assertEqual(feature.location.end, 115) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[6] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 115) self.assertEqual(feature.location.end, 136) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[7] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 136) self.assertEqual(feature.location.end, 163) self.assertEqual(feature.qualifiers["note"], "Extracellular") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[8] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 163) self.assertEqual(feature.location.end, 184) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[9] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 184) self.assertEqual(feature.location.end, 211) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250") feature = record.features[10] self.assertEqual(feature.type, "REGION") self.assertEqual(feature.location.start, 191) self.assertEqual(feature.location.end, 211) self.assertEqual(feature.qualifiers["note"], "Disordered") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000256|SAM:MobiDB-lite") feature = record.features[11] self.assertEqual(feature.type, "REGION") self.assertEqual(feature.location.start, 209) self.assertEqual(feature.location.end, 211) self.assertEqual( feature.qualifiers["note"], "Interactions with TJP1, TJP2, TJP3 and PATJ" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250") feature = record.features[12] self.assertEqual(feature.type, "DISULFID") self.assertEqual(feature.location.start, 53) self.assertEqual(feature.location.end, 64) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250") feature = record.features[13] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 31) self.assertEqual(feature.location.end, 32) self.assertEqual( feature.qualifiers["note"], "I->M: Loss of HCV receptor activity. Significant loss of interaction with CD81. Reduced interaction with OCLN.", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:17325668,ECO:0000269|PubMed:20375010", ) feature = record.features[14] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 47) self.assertEqual(feature.location.end, 48) self.assertEqual( feature.qualifiers["note"], "E->K: Loss of HCV receptor activity. Significant loss of interaction with CD81. Reduced interaction with OCLN. According to PubMed:17325668 no effect observed on HCV infection susceptibility in cell culture.", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:17325668,ECO:0000269|PubMed:20375010", ) feature = record.features[15] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 61) self.assertEqual(feature.location.end, 62) self.assertEqual(feature.qualifiers["note"], "I -> V (in Ref. 2; AAD22962)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[16] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 134) self.assertEqual(feature.location.end, 135) self.assertEqual(feature.qualifiers["note"], "V -> A (in Ref. 2; AAD22962)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 17) reference = record.references[0] self.assertEqual( reference.authors, "Swisshelm K.L., Machl A., Planitzer S., Robertson R., Kubbies M., Hosier S.", ) self.assertEqual( reference.title, "SEMP1, a senescence-associated cDNA isolated from human mammary epithelial cells, is a member of an epithelial membrane protein superfamily.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "9931503")) self.assertEqual( reference.references[1], ("DOI", "10.1016/s0378-1119(98)00553-8") ) reference = record.references[1] self.assertEqual(reference.authors, "Mitic L.M., Anderson J.M.") self.assertEqual(reference.title, "Human claudin-1 isolated from Caco-2 mRNA.") self.assertEqual(len(reference.references), 0) reference = record.references[2] self.assertEqual( reference.authors, "Halford S., Spencer P., Greenwood J., Winton H., Hunt D.M., Adamson P.", ) self.assertEqual( reference.title, "Assignment of claudin-1 (CLDN1) to human chromosome 3q28-->q29 with somatic cell hybrids.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "10828592")) self.assertEqual(reference.references[1], ("DOI", "10.1159/000015553")) reference = record.references[3] self.assertEqual( reference.authors, "Kraemer F., White K., Kubbies M., Swisshelm K.L., Weber B.H.F.", ) self.assertEqual( reference.title, "Genomic organization of claudin-1 and its assessment in hereditary and sporadic breast cancer.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "11071387")) self.assertEqual(reference.references[1], ("DOI", "10.1007/s004390000375")) reference = record.references[4] self.assertEqual( reference.authors, "Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E., Heldens S., Huang A., Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D., Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L., Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C., Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J., Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.", ) self.assertEqual( reference.title, "The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "12975309")) self.assertEqual(reference.references[1], ("DOI", "10.1101/gr.1293003")) reference = record.references[5] self.assertEqual( reference.authors, "Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.", ) self.assertEqual( reference.title, "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201).", ) self.assertEqual(len(reference.references), 0) reference = record.references[6] self.assertEqual(reference.authors, "The MGC Project Team") self.assertEqual( reference.title, "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "15489334")) self.assertEqual(reference.references[1], ("DOI", "10.1101/gr.2596504")) reference = record.references[7] self.assertEqual( reference.authors, "Hadj-Rabia S., Baala L., Vabres P., Hamel-Teillac D., Jacquemin E., Fabre M., Lyonnet S., De Prost Y., Munnich A., Hadchouel M., Smahi A.", ) self.assertEqual( reference.title, "Claudin-1 gene mutations in neonatal sclerosing cholangitis associated with ichthyosis: a tight junction disease.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "15521008")) self.assertEqual( reference.references[1], ("DOI", "10.1053/j.gastro.2004.07.022") ) reference = record.references[8] self.assertEqual( reference.authors, "Feldmeyer L., Huber M., Fellmann F., Beckmann J.S., Frenk E., Hohl D.", ) self.assertEqual( reference.title, "Confirmation of the origin of NISCH syndrome." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "16619213")) self.assertEqual(reference.references[1], ("DOI", "10.1002/humu.20333")) reference = record.references[9] self.assertEqual( reference.authors, "Evans M.J., von Hahn T., Tscherne D.M., Syder A.J., Panis M., Wolk B., Hatziioannou T., McKeating J.A., Bieniasz P.D., Rice C.M.", ) self.assertEqual( reference.title, "Claudin-1 is a hepatitis C virus co-receptor required for a late step in entry.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17325668")) self.assertEqual(reference.references[1], ("DOI", "10.1038/nature05654")) reference = record.references[10] self.assertEqual( reference.authors, "Harris H.J., Davis C., Mullins J.G., Hu K., Goodall M., Farquhar M.J., Mee C.J., McCaffrey K., Young S., Drummer H., Balfe P., McKeating J.A.", ) self.assertEqual( reference.title, "Claudin association with CD81 defines hepatitis C virus entry.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "20375010")) self.assertEqual(reference.references[1], ("DOI", "10.1074/jbc.m110.104836")) reference = record.references[11] self.assertEqual( reference.authors, "Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.", ) self.assertEqual( reference.title, "Initial characterization of the human central proteome." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21269460")) self.assertEqual(reference.references[1], ("DOI", "10.1186/1752-0509-5-17")) reference = record.references[12] self.assertEqual( reference.authors, "Lupberger J., Zeisel M.B., Xiao F., Thumann C., Fofana I., Zona L., Davis C., Mee C.J., Turek M., Gorke S., Royer C., Fischer B., Zahid M.N., Lavillette D., Fresquet J., Cosset F.L., Rothenberg S.M., Pietschmann T., Patel A.H., Pessaux P., Doffoel M., Raffelsberger W., Poch O., McKeating J.A., Brino L., Baumert T.F.", ) self.assertEqual( reference.title, "EGFR and EphA2 are host factors for hepatitis C virus entry and possible targets for antiviral therapy.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21516087")) self.assertEqual(reference.references[1], ("DOI", "10.1038/nm.2341")) reference = record.references[13] self.assertEqual( reference.authors, "Kirschner N., Rosenthal R., Furuse M., Moll I., Fromm M., Brandner J.M.", ) self.assertEqual( reference.title, "Contribution of tight junction proteins to ion, macromolecule, and water barrier in keratinocytes.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "23407391")) self.assertEqual(reference.references[1], ("DOI", "10.1038/jid.2012.507")) reference = record.references[14] self.assertEqual(reference.authors, "Che P., Tang H., Li Q.") self.assertEqual( reference.title, "The interaction between claudin-1 and dengue viral prM/M protein for its entry.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "24074594")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.virol.2013.08.009") ) reference = record.references[15] self.assertEqual( reference.authors, "Bonander N., Jamshad M., Oberthuer D., Clare M., Barwell J., Hu K., Farquhar M.J., Stamataki Z., Harris H.J., Dierks K., Dafforn T.R., Betzel C., McKeating J.A., Bill R.M.", ) self.assertEqual( reference.title, "Production, purification and characterization of recombinant, full-length human claudin-1.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "23704991")) self.assertEqual( reference.references[1], ("DOI", "10.1371/journal.pone.0064517") ) reference = record.references[16] self.assertEqual( reference.authors, "Douam F., Dao Thi V.L., Maurin G., Fresquet J., Mompelat D., Zeisel M.B., Baumert T.F., Cosset F.L., Lavillette D.", ) self.assertEqual( reference.title, "Critical interaction between E1 and E2 glycoproteins determines binding and fusion properties of hepatitis C virus during cell entry.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "24038151")) self.assertEqual(reference.references[1], ("DOI", "10.1002/hep.26733")) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_P04439(self): """Parsing SwissProt file P04439.txt.""" filename = "P04439.txt" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "P04439") self.assertEqual(seq_record.name, "HLAA_HUMAN") self.assertEqual( seq_record.description, "RecName: Full=HLA class I histocompatibility antigen, A alpha chain; AltName: Full=Human leukocyte antigen A; Short=HLA-A; Flags: Precursor;", ) self.assertEqual( repr(seq_record.seq), "Seq('MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDD...CKV')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "HLAA_HUMAN") self.assertEqual( record.accessions, [ "P04439", "B1PKZ3", "O02939", "O02954", "O02955", "O02963", "O19509", "O19546", "O19598", "O19605", "O19606", "O19619", "O19647", "O19673", "O19687", "O19695", "O19756", "O19794", "O19795", "O43906", "O43907", "O46874", "O62921", "O62924", "O77937", "O77938", "O77964", "O78073", "O78171", "O98009", "O98010", "O98011", "O98137", "P01891", "P01892", "P05534", "P06338", "P10313", "P10314", "P10315", "P10316", "P13746", "P16188", "P16189", "P16190", "P18462", "P30443", "P30444", "P30445", "P30446", "P30447", "P30448", "P30449", "P30450", "P30451", "P30452", "P30453", "P30454", "P30455", "P30456", "P30457", "P30458", "P30459", "P30512", "P30514", "P79505", "P79562", "P79563", "Q09160", "Q29680", "Q29747", "Q29835", "Q29837", "Q29838", "Q29899", "Q29908", "Q29909", "Q29910", "Q30208", "Q31623", "Q5S3G1", "Q65A82", "Q8MHM1", "Q8MHN9", "Q95352", "Q95355", "Q95362", "Q95377", "Q95380", "Q95IZ5", "Q9BCN0", "Q9BD15", "Q9BD19", "Q9GJE6", "Q9GJE7", "Q9GJE8", "Q9MW42", "Q9MY89", "Q9MYA3", "Q9MYA5", "Q9MYC4", "Q9MYE6", "Q9MYE9", "Q9MYG4", "Q9MYG5", "Q9MYI5", "Q9TP25", "Q9TPQ3", "Q9TPR8", "Q9TPX8", "Q9TPX9", "Q9TPY0", "Q9TQ24", "Q9TQE8", "Q9TQE9", "Q9TQF1", "Q9TQF5", "Q9TQF8", "Q9TQF9", "Q9TQG0", "Q9TQG5", "Q9TQG7", "Q9TQH5", "Q9TQI3", "Q9TQK5", "Q9TQM6", "Q9TQN5", "Q9TQP5", "Q9TQP6", "Q9TQP7", "Q9UIN1", "Q9UIN2", "Q9UIP7", "Q9UQU3", "Q9UQU6", "Q9UQU7", ], ) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Euarchontoglires", "Primates", "Haplorrhini", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (365, 40841, "DEDFCEC4450E0580")) self.assertEqual(len(record.features), 161) feature = record.features[0] self.assertEqual(feature.type, "SIGNAL") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 24) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:92029") feature = record.features[1] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 24) self.assertEqual(feature.location.end, 365) self.assertEqual( feature.qualifiers["note"], "HLA class I histocompatibility antigen, A alpha chain", ) feature = record.features[2] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 24) self.assertEqual(feature.location.end, 308) self.assertEqual(feature.qualifiers["note"], "Extracellular") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[3] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 308) self.assertEqual(feature.location.end, 332) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[4] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 332) self.assertEqual(feature.location.end, 365) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[5] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 208) self.assertEqual(feature.location.end, 295) self.assertEqual(feature.qualifiers["note"], "Ig-like C1-type") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[6] self.assertEqual(feature.type, "REGION") self.assertEqual(feature.location.start, 24) self.assertEqual(feature.location.end, 114) self.assertEqual(feature.qualifiers["note"], "Alpha-1") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[7] self.assertEqual(feature.type, "REGION") self.assertEqual(feature.location.start, 114) self.assertEqual(feature.location.end, 206) self.assertEqual(feature.qualifiers["note"], "Alpha-2") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[8] self.assertEqual(feature.type, "REGION") self.assertEqual(feature.location.start, 206) self.assertEqual(feature.location.end, 298) self.assertEqual(feature.qualifiers["note"], "Alpha-3") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[9] self.assertEqual(feature.type, "REGION") self.assertEqual(feature.location.start, 298) self.assertEqual(feature.location.end, 308) self.assertEqual(feature.qualifiers["note"], "Connecting peptide") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[10] self.assertEqual(feature.type, "REGION") self.assertEqual(feature.location.start, 338) self.assertEqual(feature.location.end, 365) self.assertEqual(feature.qualifiers["note"], "Disordered") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000256|SAM:MobiDB-lite") feature = record.features[11] self.assertEqual(feature.type, "COMPBIAS") self.assertEqual(feature.location.start, 340) self.assertEqual(feature.location.end, 359) self.assertEqual(feature.qualifiers["note"], "Polar residues") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000256|SAM:MobiDB-lite") feature = record.features[12] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 30) self.assertEqual(feature.location.end, 31) self.assertEqual(feature.qualifiers["ligand"], "a peptide antigen") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:166823") self.assertEqual(feature.qualifiers["ligand_label"], "1") self.assertEqual( feature.qualifiers["ligand_note"], "pathogen-derived peptide antigen" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21943705") feature = record.features[13] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 96) self.assertEqual(feature.location.end, 97) self.assertEqual(feature.qualifiers["ligand"], "a peptide antigen") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:166823") self.assertEqual(feature.qualifiers["ligand_label"], "1") self.assertEqual( feature.qualifiers["ligand_note"], "pathogen-derived peptide antigen" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21943705") feature = record.features[14] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 107) self.assertEqual(feature.location.end, 108) self.assertEqual(feature.qualifiers["ligand"], "a peptide antigen") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:166823") self.assertEqual(feature.qualifiers["ligand_label"], "1") self.assertEqual( feature.qualifiers["ligand_note"], "pathogen-derived peptide antigen" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21943705") feature = record.features[15] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 139) self.assertEqual(feature.location.end, 140) self.assertEqual(feature.qualifiers["ligand"], "a peptide antigen") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:166823") self.assertEqual(feature.qualifiers["ligand_label"], "2") self.assertEqual(feature.qualifiers["ligand_note"], "self-peptide antigen") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21543847") feature = record.features[16] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 166) self.assertEqual(feature.location.end, 167) self.assertEqual(feature.qualifiers["ligand"], "a peptide antigen") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:166823") self.assertEqual(feature.qualifiers["ligand_label"], "1") self.assertEqual( feature.qualifiers["ligand_note"], "pathogen-derived peptide antigen" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21943705") feature = record.features[17] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 169) self.assertEqual(feature.location.end, 170) self.assertEqual(feature.qualifiers["ligand"], "a peptide antigen") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:166823") self.assertEqual(feature.qualifiers["ligand_label"], "1") self.assertEqual( feature.qualifiers["ligand_note"], "pathogen-derived peptide antigen" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21943705") feature = record.features[18] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 182) self.assertEqual(feature.location.end, 183) self.assertEqual(feature.qualifiers["ligand"], "a peptide antigen") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:166823") self.assertEqual(feature.qualifiers["ligand_label"], "1") self.assertEqual( feature.qualifiers["ligand_note"], "pathogen-derived peptide antigen" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21943705") feature = record.features[19] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 182) self.assertEqual(feature.location.end, 183) self.assertEqual(feature.qualifiers["ligand"], "a peptide antigen") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:166823") self.assertEqual(feature.qualifiers["ligand_label"], "2") self.assertEqual(feature.qualifiers["ligand_note"], "self-peptide antigen") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21543847") feature = record.features[20] self.assertEqual(feature.type, "BINDING") self.assertEqual(feature.location.start, 194) self.assertEqual(feature.location.end, 195) self.assertEqual(feature.qualifiers["ligand"], "a peptide antigen") self.assertEqual(feature.qualifiers["ligand_id"], "ChEBI:CHEBI:166823") self.assertEqual(feature.qualifiers["ligand_label"], "1") self.assertEqual( feature.qualifiers["ligand_note"], "pathogen-derived peptide antigen" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21943705") feature = record.features[21] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 82) self.assertEqual(feature.location.end, 83) self.assertEqual(feature.qualifiers["note"], "Sulfotyrosine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[22] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 342) self.assertEqual(feature.location.end, 343) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0007744|PubMed:24275569") feature = record.features[23] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 343) self.assertEqual(feature.location.end, 344) self.assertEqual(feature.qualifiers["note"], "Phosphotyrosine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0007744|PubMed:24275569") feature = record.features[24] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 348) self.assertEqual(feature.location.end, 349) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0007744|PubMed:24275569") feature = record.features[25] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 349) self.assertEqual(feature.location.end, 350) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0007744|PubMed:24275569") feature = record.features[26] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 351) self.assertEqual(feature.location.end, 352) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0007744|PubMed:24275569") feature = record.features[27] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 355) self.assertEqual(feature.location.end, 356) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual( feature.qualifiers["evidence"], "ECO:0007744|PubMed:23186163,ECO:0007744|PubMed:24275569", ) feature = record.features[28] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 358) self.assertEqual(feature.location.end, 359) self.assertEqual(feature.qualifiers["note"], "Phosphoserine") self.assertEqual( feature.qualifiers["evidence"], "ECO:0007744|PubMed:23186163,ECO:0007744|PubMed:24275569", ) feature = record.features[29] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 109) self.assertEqual(feature.location.end, 110) self.assertEqual(feature.qualifiers["note"], "N-linked (GlcNAc...) asparagine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:19159218") feature = record.features[30] self.assertEqual(feature.type, "DISULFID") self.assertEqual(feature.location.start, 124) self.assertEqual(feature.location.end, 188) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|PROSITE-ProRule:PRU00114,ECO:0000269|PubMed:16041067, ECO:0000269|PubMed:19177349,ECO:0000269|PubMed:20844028, ECO:0000269|PubMed:21543847,ECO:0000269|PubMed:21943705, ECO:0000269|PubMed:26758806,ECO:0000269|PubMed:28250417, ECO:0000269|PubMed:7694806", ) feature = record.features[31] self.assertEqual(feature.type, "DISULFID") self.assertEqual(feature.location.start, 226) self.assertEqual(feature.location.end, 283) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|PROSITE-ProRule:PRU00114,ECO:0000269|PubMed:16041067, ECO:0000269|PubMed:19177349,ECO:0000269|PubMed:20844028, ECO:0000269|PubMed:21543847,ECO:0000269|PubMed:21943705, ECO:0000269|PubMed:26758806,ECO:0000269|PubMed:28250417, ECO:0000269|PubMed:7694806", ) feature = record.features[32] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 187) self.assertEqual( feature.qualifiers["note"], "EAEQLRAYLDGT -> AAEQQRAYLEGR (in isoform 2)" ) feature = record.features[33] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 336) self.assertEqual(feature.location.end, 337) self.assertEqual(feature.qualifiers["note"], "S -> SGGEGVK (in isoform 2)") feature = record.features[34] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 2) self.assertEqual(feature.location.end, 3) self.assertEqual(feature.qualifiers["note"], "V -> I (in allele A*34:01)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115") feature = record.features[35] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 4) self.assertEqual(feature.location.end, 5) self.assertEqual(feature.qualifiers["note"], "A -> P (in allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[36] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 9) self.assertEqual(feature.location.end, 10) self.assertEqual( feature.qualifiers["note"], "L -> V (in allele A*02:01, allele A*02:05, allele A*23:01, allele A*24:02, allele A*25:01, allele A*26:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01 and allele A*69:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:1729171, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:7836067,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8475492,ECO:0000269|PubMed:9349616", ) feature = record.features[37] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 13) self.assertEqual(feature.location.end, 14) self.assertEqual( feature.qualifiers["note"], "S -> L (in allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:8795145, ECO:0000269|Ref.29", ) feature = record.features[38] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 22) self.assertEqual(feature.location.end, 23) self.assertEqual(feature.qualifiers["note"], "W -> R (in allele A*74:01)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115") feature = record.features[39] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 32) self.assertEqual(feature.location.end, 33) self.assertEqual( feature.qualifiers["note"], "F -> S (in allele A*23:01, allele A*24:02 and allele A*30:01; dbSNP:rs2075684)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:7871528,ECO:0000269|PubMed:9349616", ) feature = record.features[40] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 32) self.assertEqual(feature.location.end, 33) self.assertEqual( feature.qualifiers["note"], "F -> T (in allele A*29:02, allele A*31:01 and allele A*33:01; requires 2 nucleotide substitutions)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:8795145", ) feature = record.features[41] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 32) self.assertEqual(feature.location.end, 33) self.assertEqual( feature.qualifiers["note"], "F -> Y (in allele A*02:05, allele A*11:01, allele A*25:01, allele A*26:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01 and allele A*69:01; dbSNP:rs2075684)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2437024,ECO:0000269|PubMed:2460344, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:8016845,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8475492", ) feature = record.features[42] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 40) self.assertEqual(feature.location.end, 41) self.assertEqual( feature.qualifiers["note"], "R -> S (in allele A*30:01; dbSNP:rs1059423)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:7871528", ) feature = record.features[43] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 54) self.assertEqual(feature.location.end, 55) self.assertEqual(feature.qualifiers["note"], "T -> S (in allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[44] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 58) self.assertEqual(feature.location.end, 59) self.assertEqual(feature.qualifiers["note"], "R -> Q (in allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[45] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 66) self.assertEqual(feature.location.end, 67) self.assertEqual( feature.qualifiers["note"], "Q -> R (in allele A*02:05; dbSNP:rs41559117)" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:3496393") feature = record.features[46] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 67) self.assertEqual(feature.location.end, 68) self.assertEqual( feature.qualifiers["note"], "R -> K (in alleles A*01:01 and allele A*36:01)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:9349617", ) feature = record.features[47] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 79) self.assertEqual(feature.location.end, 80) self.assertEqual(feature.qualifiers["note"], "G -> E (in allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[48] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 79) self.assertEqual(feature.location.end, 80) self.assertEqual( feature.qualifiers["note"], "G -> R (in allele A*30:01 and allele A*31:01; dbSNP:rs1059449)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:7871528,ECO:0000269|PubMed:8795145", ) feature = record.features[49] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 85) self.assertEqual(feature.location.end, 86) self.assertEqual( feature.qualifiers["note"], "Q -> E (in allele A*23:01, allele 24:02 and allele A*80:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:8188325, ECO:0000269|PubMed:8284791,ECO:0000269|PubMed:9349616", ) feature = record.features[50] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 85) self.assertEqual(feature.location.end, 86) self.assertEqual( feature.qualifiers["note"], "Q -> G (in allele A*02:01 and allele A*02:05; requires 2 nucleotide substitutions)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:7836067", ) feature = record.features[51] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 85) self.assertEqual(feature.location.end, 86) self.assertEqual( feature.qualifiers["note"], "Q -> L (in alleles A*29:02 and allele A*43:01)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:1782566", ) feature = record.features[52] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 85) self.assertEqual(feature.location.end, 86) self.assertEqual( feature.qualifiers["note"], "Q -> R (in allele A*25:01, allele A*26:01, allele A*33:01, allele A*34:01, allele A*66:01, allele A*68:01 and allele A*69:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492", ) feature = record.features[53] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 86) self.assertEqual(feature.location.end, 87) self.assertEqual( feature.qualifiers["note"], "E -> N (in alleles A*25:01, allele A*26:01, allele A*33:01, allele A*34:01, allele A*66:01, allele A*68:01 and allele A*69:01; requires 2 nucleotide substitutions)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492", ) feature = record.features[54] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 86) self.assertEqual(feature.location.end, 87) self.assertEqual( feature.qualifiers["note"], "E -> Q (in allele A*29:02 and allele A*43:01)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:1782566", ) feature = record.features[55] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 88) self.assertEqual(feature.location.end, 89) self.assertEqual( feature.qualifiers["note"], "R -> G (in allele A*23:01 and allele 24:02; dbSNP:rs199474430)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:9349616", ) feature = record.features[56] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 89) self.assertEqual(feature.location.end, 90) self.assertEqual( feature.qualifiers["note"], "N -> K (in allele A*02:01, allele A*02:05, allele A*23:01, allele 24:02 and allele A*34:01; dbSNP:rs199474436)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:1729171, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:9349616", ) feature = record.features[57] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 90) self.assertEqual(feature.location.end, 91) self.assertEqual( feature.qualifiers["note"], "V -> M (in allele A*01:01 and allele A*36:01)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:9349617", ) feature = record.features[58] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 93) self.assertEqual(feature.location.end, 94) self.assertEqual( feature.qualifiers["note"], "Q -> H (in allele A*01:01, allele A*02:01, allele A*02:05, allele A*23:01, allele 24:02, allele A*25:01, allele A*26:01, allele A*31:01, allele A*32:01, allele A*33:01, allele A*36:01, allele A*43:01, allele A*74:01 and allele A*80:01; dbSNP:rs78306866)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:2715640, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:7836067,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791, ECO:0000269|PubMed:8475492,ECO:0000269|PubMed:8795145, ECO:0000269|PubMed:9349616,ECO:0000269|PubMed:9349617, ECO:0000269|Ref.29", ) feature = record.features[59] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 96) self.assertEqual(feature.location.end, 97) self.assertEqual( feature.qualifiers["note"], "T -> I (in allele A*31:01 and allele A*33:01; dbSNP:rs199474457)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:8795145", ) feature = record.features[60] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 97) self.assertEqual(feature.location.end, 98) self.assertEqual( feature.qualifiers["note"], "D -> H (in allele A*02:01 and allele A*02:05)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:7836067", ) feature = record.features[61] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 97) self.assertEqual(feature.location.end, 98) self.assertEqual(feature.qualifiers["note"], "D -> N (in allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[62] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 99) self.assertEqual(feature.location.end, 100) self.assertEqual( feature.qualifiers["note"], "V -> A (in allele A*01:01, allele A*26:01, allele A*29:02, allele A*36:01, allele A*43:01 and allele A*80:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2251137,ECO:0000269|PubMed:2715640, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8188325, ECO:0000269|PubMed:8284791,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:9349617", ) feature = record.features[63] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 99) self.assertEqual(feature.location.end, 100) self.assertEqual( feature.qualifiers["note"], "V -> E (in allele A*23:01, allele A*24:02, allele A*25:01 and allele A*32:01; dbSNP:rs1071742)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:9349616, ECO:0000269|Ref.29", ) feature = record.features[64] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 100) self.assertEqual(feature.location.end, 101) self.assertEqual( feature.qualifiers["note"], "D -> N (allele A*01:01, allele A*23:01, allele A*24:02, allele A*26:01, allele A*29:02, allele A*36:01, allele A*43:01 and allele A*80:01; dbSNP:rs1136688)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:1729171, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791, ECO:0000269|PubMed:8475492,ECO:0000269|PubMed:9349616, ECO:0000269|PubMed:9349617", ) feature = record.features[65] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 100) self.assertEqual(feature.location.end, 101) self.assertEqual( feature.qualifiers["note"], "D -> S (in allele A*25:01 and allele A*32:01; requires 2 nucleotide substitutions)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|Ref.29", ) feature = record.features[66] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 102) self.assertEqual(feature.location.end, 107) self.assertEqual( feature.qualifiers["note"], "GTLRG -> RIALR (in allele A*23:01, allele A*24:02, allele A*25:01 and allele A*32:01; Bw4 motif RIALR is involved in the recognition of NK cell inhibitory receptor KIR3DL1)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:17182537,ECO:0000269|PubMed:1729171, ECO:0000269|PubMed:18502829,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:9349616, ECO:0000269|Ref.29", ) feature = record.features[67] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 113) self.assertEqual(feature.location.end, 114) self.assertEqual( feature.qualifiers["note"], "A -> D (in allele A*01:01, allele A*11:01, allele A*25:01, allele A*26:01, allele A*34:01, allele A*36:01, allele A*43:01, allele A*66:01 and allele A*80:01; dbSNP:rs1136692)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2437024, ECO:0000269|PubMed:2460344,ECO:0000269|PubMed:2715640, ECO:0000269|PubMed:8016845,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791, ECO:0000269|PubMed:8475492,ECO:0000269|PubMed:9349617", ) feature = record.features[68] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 118) self.assertEqual(feature.location.end, 119) self.assertEqual( feature.qualifiers["note"], "I -> L (in allele A*02:05, allele A*23:01 and allele 24:02; dbSNP:rs1071743)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:9349616", ) feature = record.features[69] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 118) self.assertEqual(feature.location.end, 119) self.assertEqual( feature.qualifiers["note"], "I -> V (in allele A*02:01 and allele A*69:01)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067", ) feature = record.features[70] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 120) self.assertEqual(feature.location.end, 121) self.assertEqual( feature.qualifiers["note"], "I -> M (in allele A*23:01, allele 24:02, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*68:01 and allele A*74:01; dbSNP:rs1136695)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:8795145, ECO:0000269|PubMed:9349616,ECO:0000269|Ref.29", ) feature = record.features[71] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 120) self.assertEqual(feature.location.end, 121) self.assertEqual( feature.qualifiers["note"], "I -> R (in allele A*02:01, allele A*02:05, allele A*25:01, allele A*26:01, allele A*34:01, allele A*43:01, allele A*66:01 and allele A*69:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492", ) feature = record.features[72] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 122) self.assertEqual(feature.location.end, 123) self.assertEqual( feature.qualifiers["note"], "Y -> F (in allele A*23:01, allele 24:02; dbSNP:rs1136697)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:9349616", ) feature = record.features[73] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 128) self.assertEqual(feature.location.end, 129) self.assertEqual( feature.qualifiers["note"], "S -> P (in allele A*01:01, allele A*11:01, allele A*25:01, allele A*26:01, allele A*32:01, allele A*34:01, allele A*36:01, allele A*43:01, allele A*66:01 and allele A*74:01; dbSNP:rs1136700)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2437024,ECO:0000269|PubMed:2460344, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:8016845, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:9349617,ECO:0000269|Ref.29", ) feature = record.features[74] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 130) self.assertEqual(feature.location.end, 131) self.assertEqual( feature.qualifiers["note"], "G -> W (in allele A*02:01, allele A*02:05 and allele A*69:01; dbSNP:rs1136702)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:7836067", ) feature = record.features[75] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 132) self.assertEqual(feature.location.end, 133) self.assertEqual( feature.qualifiers["note"], "F -> L (in allele A*32:01 and allele A*74:01; dbSNP:rs1059488)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2431040, ECO:0000269|Ref.29", ) feature = record.features[76] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 137) self.assertEqual(feature.location.end, 138) self.assertEqual( feature.qualifiers["note"], "R -> E (in allele A*30:01; requires 2 nucleotide substitutions)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:7871528", ) feature = record.features[77] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 137) self.assertEqual(feature.location.end, 138) self.assertEqual( feature.qualifiers["note"], "R -> H (in allele A*02:01, allele A*02:05, allele A*23:01, allele A*24:02, allele A*69:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:9349616", ) feature = record.features[78] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 137) self.assertEqual(feature.location.end, 138) self.assertEqual( feature.qualifiers["note"], "R -> Q (in allele A*25:01, allele A*26:01, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8475492,ECO:0000269|PubMed:8795145, ECO:0000269|Ref.29", ) feature = record.features[79] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 139) self.assertEqual(feature.location.end, 140) self.assertEqual(feature.qualifiers["note"], "D -> H (in allele A*30:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:7871528", ) feature = record.features[80] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 139) self.assertEqual(feature.location.end, 140) self.assertEqual( feature.qualifiers["note"], "D -> Y (in allele A*02:01, allele A*02:05, allele A*23:01, allele A*24:02 and allele A*69:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:9349616", ) feature = record.features[81] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 150) self.assertEqual(feature.location.end, 151) self.assertEqual( feature.qualifiers["note"], "N -> K (in allele A*02:01, allele A*02:05, allele A*23:01, allele A*24:02, allele A*68:01 and allele A*69:01; dbSNP:rs1059509)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:9349616", ) feature = record.features[82] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 165) self.assertEqual(feature.location.end, 166) self.assertEqual( feature.qualifiers["note"], "I -> T (in allele A*02:01, allele A*02:05, allele A*68:01 and allele A*69:01; dbSNP:rs1059516)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:7836067", ) feature = record.features[83] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 167) self.assertEqual(feature.location.end, 168) self.assertEqual( feature.qualifiers["note"], "K -> Q (in allele A*23:01, allele A*25:01, allele A*26:01, allele A*29:02, allele A*30:01, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:7871528, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:8795145,ECO:0000269|Ref.29", ) feature = record.features[84] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 168) self.assertEqual(feature.location.end, 169) self.assertEqual( feature.qualifiers["note"], "R -> H (in allele A*02:01, allele A*02:05, allele A*68:01 and allele A*69:01; dbSNP:rs1059520)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:7836067", ) feature = record.features[85] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 172) self.assertEqual(feature.location.end, 173) self.assertEqual( feature.qualifiers["note"], "A -> T (in allele A*25:01, allele A*26:01, allele A*34:01, allele A*43:01 and allele A*66:01; dbSNP:rs1059526)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492", ) feature = record.features[86] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 173) self.assertEqual(feature.location.end, 174) self.assertEqual( feature.qualifiers["note"], "A -> V (in allele A*01:01 and allele A*36:01)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:9349617", ) feature = record.features[87] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 174) self.assertEqual(feature.location.end, 175) self.assertEqual( feature.qualifiers["note"], "H -> R (in allele A*23:01, allele A*29:02, allele A*30:01, allele A*31:01, allele A*32:01, allele A*33:01, allele A*74:01 and allele A*80:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:7871528,ECO:0000269|PubMed:8188325, ECO:0000269|PubMed:8284791,ECO:0000269|PubMed:8795145, ECO:0000269|Ref.29", ) feature = record.features[88] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 176) self.assertEqual( feature.qualifiers["note"], "E -> A (in allele A*01:01, allele A*11:01 and allele A*36:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2437024,ECO:0000269|PubMed:2460344, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:8016845, ECO:0000269|PubMed:9349617", ) feature = record.features[89] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 176) self.assertEqual( feature.qualifiers["note"], "E -> R (in allele A*80:01; requires 2 nucleotide substitutions)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[90] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 176) self.assertEqual( feature.qualifiers["note"], "E -> V (in allele A*02:01, allele A*02:05, allele A*23:01, allele A*24:02, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*68:01, allele A*69:01 and allele A*74:01; results in inefficient T cell recognition of epitopes derived from influenza A virus.; dbSNP:rs9256983)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2456340,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:8795145,ECO:0000269|PubMed:9349616, ECO:0000269|Ref.29", ) feature = record.features[91] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 176) self.assertEqual( feature.qualifiers["note"], "E -> W (in allele A*30:01; requires 2 nucleotide substitutions)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:7871528", ) feature = record.features[92] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 179) self.assertEqual(feature.location.end, 180) self.assertEqual( feature.qualifiers["note"], "L -> Q (in allele A*11:01 and allele A*24:02)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:2437024, ECO:0000269|PubMed:2460344,ECO:0000269|PubMed:8016845, ECO:0000269|PubMed:9349616", ) feature = record.features[93] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 179) self.assertEqual(feature.location.end, 180) self.assertEqual( feature.qualifiers["note"], "L -> R (in allele A*01:01 and allele A*36:01)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:9349617", ) feature = record.features[94] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 179) self.assertEqual(feature.location.end, 180) self.assertEqual( feature.qualifiers["note"], "L -> W (in allele A*02:05, allele A*25:01, allele A*26:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01; dbSNP:rs9260156)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492", ) feature = record.features[95] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 181) self.assertEqual(feature.location.end, 182) self.assertEqual( feature.qualifiers["note"], "A -> V (in allele A*01:01 and allele A*36:01)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:9349617", ) feature = record.features[96] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 184) self.assertEqual(feature.location.end, 185) self.assertEqual( feature.qualifiers["note"], "D -> E (in allele A*01:01, allele A*02:01, allele A*02:05, allele A*11:01, allele A*23:01, allele A*24:02, allele A*25:01, allele A*26:01, allele A*29:02, allele A*30:01, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*36:01, allele A*43:01, allele A*66:01, allele A*68:01, allele A*69:01, allele A*74:01 and allele A*80:01; dbSNP:rs1059542)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2251137,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2437024, ECO:0000269|PubMed:2460344,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:7836067,ECO:0000269|PubMed:7871528, ECO:0000269|PubMed:8016845,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791, ECO:0000269|PubMed:8475492,ECO:0000269|PubMed:8795145, ECO:0000269|PubMed:9349616,ECO:0000269|PubMed:9349617, ECO:0000269|Ref.29", ) feature = record.features[97] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 186) self.assertEqual(feature.location.end, 187) self.assertEqual( feature.qualifiers["note"], "T -> E (in allele A*80:01; requires 2 nucleotide substitutions)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[98] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 186) self.assertEqual(feature.location.end, 187) self.assertEqual( feature.qualifiers["note"], "T -> R (in allele A*01:01, allele A*11:01, allele A*25:01, allele A*26:01, allele A*43:01 and allele A*66:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2437024, ECO:0000269|PubMed:2460344,ECO:0000269|PubMed:2715640, ECO:0000269|PubMed:8016845,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8475492,ECO:0000269|PubMed:9349617", ) feature = record.features[99] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 189) self.assertEqual(feature.location.end, 190) self.assertEqual( feature.qualifiers["note"], "E -> D (in allele A*01:01, allele A*23:01, allele A*24:02 and allele A*80:01; dbSNP:rs879577815)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:8188325, ECO:0000269|PubMed:8284791,ECO:0000269|PubMed:9349616, ECO:0000269|PubMed:9349617", ) feature = record.features[100] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 190) self.assertEqual(feature.location.end, 191) self.assertEqual( feature.qualifiers["note"], "W -> G (in allele A*01:01, allele A*23:01, allele A*24:02 and allele A*80:01; dbSNP:rs3098019)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:2251137, ECO:0000269|PubMed:2715640,ECO:0000269|PubMed:8188325, ECO:0000269|PubMed:8284791,ECO:0000269|PubMed:9349616, ECO:0000269|PubMed:9349617", ) feature = record.features[101] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 194) self.assertEqual(feature.location.end, 195) self.assertEqual(feature.qualifiers["note"], "Y -> H (in allele A*33:01)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:2478623") feature = record.features[102] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 207) self.assertEqual(feature.location.end, 208) self.assertEqual( feature.qualifiers["note"], "P -> A (in allele A*02:01, allele A*02:05, allele A*25:01, allele A*26:01, allele A*29:02, allele A*32:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01, allele A*69:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492, ECO:0000269|Ref.29", ) feature = record.features[103] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 209) self.assertEqual(feature.location.end, 210) self.assertEqual(feature.qualifiers["note"], "K -> R (in allele A*33:01)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:2478623") feature = record.features[104] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 216) self.assertEqual(feature.location.end, 217) self.assertEqual( feature.qualifiers["note"], "P -> A (in allele A*02:01, allele A*02:05, allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01, allele A*69:01, allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:8795145,ECO:0000269|Ref.29", ) feature = record.features[105] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 217) self.assertEqual(feature.location.end, 218) self.assertEqual( feature.qualifiers["note"], "I -> V (in allele A*02:01, allele A*02:05, allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01, allele A*69:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:8795145,ECO:0000269|Ref.29", ) feature = record.features[106] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 230) self.assertEqual(feature.location.end, 231) self.assertEqual( feature.qualifiers["note"], "G -> S (in allele A*02:01, allele A*02:05, allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01, allele A*69:01, allele A*74:01 and allele A*80:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8188325, ECO:0000269|PubMed:8284791,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:8795145,ECO:0000269|Ref.29", ) feature = record.features[107] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 268) self.assertEqual(feature.location.end, 269) self.assertEqual( feature.qualifiers["note"], "A -> V (in allele A*68:01; impairs binding to CD8A and reduces recognition by antigen-specific CD8-positive T cells)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2784196,ECO:0000269|PubMed:3877632", ) feature = record.features[108] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 269) self.assertEqual(feature.location.end, 270) self.assertEqual( feature.qualifiers["note"], "A -> S (in allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8475492,ECO:0000269|Ref.29", ) feature = record.features[109] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 276) self.assertEqual(feature.location.end, 277) self.assertEqual(feature.qualifiers["note"], "E -> K (in allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[110] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 276) self.assertEqual(feature.location.end, 277) self.assertEqual( feature.qualifiers["note"], "E -> Q (in allele A*02:01, allele A*02:05, allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01, allele A*69:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:8795145,ECO:0000269|Ref.29", ) feature = record.features[111] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 278) self.assertEqual(feature.location.end, 279) self.assertEqual(feature.qualifiers["note"], "Q -> K (in allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[112] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 291) self.assertEqual(feature.location.end, 292) self.assertEqual(feature.qualifiers["note"], "K -> E (in allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[113] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 299) self.assertEqual(feature.location.end, 300) self.assertEqual( feature.qualifiers["note"], "L -> P (in allele A*02:01, allele A*02:05, allele A*23:01, allele A*24:02, allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01, allele A*69:01, allele A*74:01 and allele A*80:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:7836067,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791, ECO:0000269|PubMed:8475492,ECO:0000269|PubMed:8795145, ECO:0000269|PubMed:9349616,ECO:0000269|Ref.29", ) feature = record.features[114] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 305) self.assertEqual(feature.location.end, 306) self.assertEqual( feature.qualifiers["note"], "I -> V (in allele A*23:01 and allele A*24:02)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:9349616", ) feature = record.features[115] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 306) self.assertEqual(feature.location.end, 307) self.assertEqual(feature.qualifiers["note"], "P -> H (in allele A*23:01)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171") feature = record.features[116] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 311) self.assertEqual(feature.location.end, 312) self.assertEqual(feature.qualifiers["note"], "I -> L (in allele A*34:01)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115") feature = record.features[117] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 317) self.assertEqual(feature.location.end, 318) self.assertEqual( feature.qualifiers["note"], "L -> F (in allele A*02:01, allele A*02:05, allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01, allele A*69:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:2982951,ECO:0000269|PubMed:3496393, ECO:0000269|PubMed:3877632,ECO:0000269|PubMed:7836067, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:8795145,ECO:0000269|Ref.29", ) feature = record.features[118] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 320) self.assertEqual(feature.location.end, 321) self.assertEqual( feature.qualifiers["note"], "V -> M (in allele A*32:01 and allele A*74:01)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1431115,ECO:0000269|PubMed:2431040, ECO:0000269|Ref.29", ) feature = record.features[119] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 321) self.assertEqual(feature.location.end, 322) self.assertEqual( feature.qualifiers["note"], "I -> F (in allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:8795145, ECO:0000269|Ref.29", ) feature = record.features[120] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 322) self.assertEqual(feature.location.end, 323) self.assertEqual( feature.qualifiers["note"], "T -> A (in allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*74:01 and allele A*80:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8188325, ECO:0000269|PubMed:8284791,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:8795145,ECO:0000269|Ref.29", ) feature = record.features[121] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 330) self.assertEqual(feature.location.end, 331) self.assertEqual( feature.qualifiers["note"], "M -> R (in allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:8795145, ECO:0000269|Ref.29", ) feature = record.features[122] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 333) self.assertEqual(feature.location.end, 334) self.assertEqual(feature.qualifiers["note"], "R -> K (allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[123] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 334) self.assertEqual(feature.location.end, 335) self.assertEqual( feature.qualifiers["note"], "K -> N (in allele A*23:01 and allele A*24:02)" ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:9349616", ) feature = record.features[124] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 337) self.assertEqual(feature.location.end, 338) self.assertEqual(feature.qualifiers["note"], "D -> V (allele A*80:01)") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791", ) feature = record.features[125] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 344) self.assertEqual(feature.location.end, 345) self.assertEqual( feature.qualifiers["note"], "T -> S (in allele A*02:01, allele A*02:05, allele A*23:01, allele A*24:02, allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01, allele A*68:01 allele A*69:01, allele A*74:01 and allele A*80:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1729171,ECO:0000269|PubMed:1782566, ECO:0000269|PubMed:2320591,ECO:0000269|PubMed:2431040, ECO:0000269|PubMed:2478623,ECO:0000269|PubMed:2982951, ECO:0000269|PubMed:3496393,ECO:0000269|PubMed:3877632, ECO:0000269|PubMed:7836067,ECO:0000269|PubMed:8026990, ECO:0000269|PubMed:8188325,ECO:0000269|PubMed:8284791, ECO:0000269|PubMed:8475492,ECO:0000269|PubMed:8795145, ECO:0000269|PubMed:9349616,ECO:0000269|Ref.29", ) feature = record.features[126] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 357) self.assertEqual(feature.location.end, 358) self.assertEqual( feature.qualifiers["note"], "V -> M (in allele A*25:01, allele A*26:01, allele A*29:02, allele A*31:01, allele A*32:01, allele A*33:01, allele A*34:01, allele A*43:01, allele A*66:01 and allele A*74:01)", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:1317015,ECO:0000269|PubMed:1431115, ECO:0000269|PubMed:1782566,ECO:0000269|PubMed:2320591, ECO:0000269|PubMed:2431040,ECO:0000269|PubMed:2478623, ECO:0000269|PubMed:8026990,ECO:0000269|PubMed:8475492, ECO:0000269|PubMed:8795145,ECO:0000269|Ref.29", ) feature = record.features[127] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 109) self.assertEqual(feature.location.end, 110) self.assertEqual( feature.qualifiers["note"], "N->Q: Impairs the recruitment of HLA-A*02 in the peptide-loading complex.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:21263072") feature = record.features[128] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 155) self.assertEqual(feature.location.end, 156) self.assertEqual( feature.qualifiers["note"], "S->C: Impairs the maturation of a peptide-receptive HLA-A*02-B2M complex.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:8805302") feature = record.features[129] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 157) self.assertEqual(feature.location.end, 158) self.assertEqual( feature.qualifiers["note"], "T->K: Impairs binding to TAP1-TAP2 transporter, resulting in impaired presentation of intracellular peptides.", ) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:8630735,ECO:0000269|PubMed:8805302", ) feature = record.features[130] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 26) self.assertEqual(feature.location.end, 36) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[131] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 40) self.assertEqual(feature.location.end, 43) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[132] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 44) self.assertEqual(feature.location.end, 52) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[133] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 54) self.assertEqual(feature.location.end, 61) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[134] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 63) self.assertEqual(feature.location.end, 66) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[135] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 69) self.assertEqual(feature.location.end, 73) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4F7T") feature = record.features[136] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 73) self.assertEqual(feature.location.end, 78) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[137] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 80) self.assertEqual(feature.location.end, 108) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[138] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 112) self.assertEqual(feature.location.end, 115) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3D25") feature = record.features[139] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 117) self.assertEqual(feature.location.end, 127) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[140] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 130) self.assertEqual(feature.location.end, 142) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[141] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 144) self.assertEqual(feature.location.end, 150) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[142] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 151) self.assertEqual(feature.location.end, 155) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:6EWA") feature = record.features[143] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 156) self.assertEqual(feature.location.end, 159) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[144] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 161) self.assertEqual(feature.location.end, 173) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[145] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 184) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[146] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 186) self.assertEqual(feature.location.end, 198) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[147] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 199) self.assertEqual(feature.location.end, 203) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[148] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 209) self.assertEqual(feature.location.end, 235) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[149] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 237) self.assertEqual(feature.location.end, 243) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[150] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 245) self.assertEqual(feature.location.end, 248) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[151] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 248) self.assertEqual(feature.location.end, 251) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:2GTW") feature = record.features[152] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 251) self.assertEqual(feature.location.end, 254) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[153] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 260) self.assertEqual(feature.location.end, 263) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[154] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 264) self.assertEqual(feature.location.end, 274) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[155] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 274) self.assertEqual(feature.location.end, 277) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4JFD") feature = record.features[156] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 277) self.assertEqual(feature.location.end, 280) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[157] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 280) self.assertEqual(feature.location.end, 286) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[158] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 289) self.assertEqual(feature.location.end, 292) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:2V2X") feature = record.features[159] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 293) self.assertEqual(feature.location.end, 297) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:3MRE") feature = record.features[160] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 347) self.assertEqual(feature.location.end, 350) self.assertEqual(feature.qualifiers["evidence"], "ECO:0007829|PDB:4EN2") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 103) reference = record.references[0] self.assertEqual(reference.authors, "Wan A.M., Ennis P., Parham P., Holmes N.") self.assertEqual( reference.title, "The primary structure of HLA-A32 suggests a region involved in formation of the Bw4/Bw6 epitopes.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "2431040")) reference = record.references[1] self.assertEqual( reference.authors, "Holmes N., Ennis P., Wan A.M., Denney D.W., Parham P." ) self.assertEqual( reference.title, "Multiple genetic mechanisms have contributed to the generation of the HLA-A2/A28 family of class I MHC molecules.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "3496393")) reference = record.references[2] self.assertEqual( reference.authors, "Mayer W.E., Jonker M., Klein D., Ivanyi P., van Seventer G., Klein J.", ) self.assertEqual( reference.title, "Nucleotide sequences of chimpanzee MHC class I alleles: evidence for trans-species mode of evolution.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2460344")) self.assertEqual( reference.references[1], ("DOI", "10.1002/j.1460-2075.1988.tb03131.x") ) reference = record.references[3] self.assertEqual( reference.authors, "Trapani J.A., Mizuno S., Kang S.H., Yang S.Y., Dupont B.", ) self.assertEqual( reference.title, "Molecular mapping of a new public HLA class I epitope shared by all HLA-B and HLA-C antigens and defined by a monoclonal antibody.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2461903")) self.assertEqual(reference.references[1], ("DOI", "10.1007/bf02341610")) reference = record.references[4] self.assertEqual( reference.authors, "Kato K., Trapani J.A., Allopenna J., Dupont B., Yang S.Y.", ) self.assertEqual( reference.title, "Molecular analysis of the serologically defined HLA-Aw19 antigens. A genetically distinct family of HLA-A antigens comprising A29, A31, A32, and Aw33, but probably not A30.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "2478623")) reference = record.references[5] self.assertEqual( reference.authors, "Parham P., Lawlor D.A., Lomen C.E., Ennis P.D." ) self.assertEqual( reference.title, "Diversity and diversification of HLA-A,B,C alleles." ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "2715640")) reference = record.references[6] self.assertEqual( reference.authors, "Ennis P.D., Zemmour J., Salter R.D., Parham P." ) self.assertEqual( reference.title, "Rapid cloning of HLA-A,B cDNA by using the polymerase chain reaction: frequency and nature of errors produced in amplification.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2320591")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.87.7.2833")) reference = record.references[7] self.assertEqual( reference.authors, "Tabary T., Prochnicka-Chalufour A., Cornillet P., Lehoang P., Betuel H., Cohen H.M.", ) self.assertEqual( reference.title, "HLA-A29 sub-types and 'Birdshot' choroido-retinopathy susceptibility: a possible 'resistance motif' in the HLA-A29.1 molecule.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "1782566")) reference = record.references[8] self.assertEqual(reference.authors, "Little A.-M., Madrigal J.A., Parham P.") self.assertEqual( reference.title, "Molecular definition of an elusive third HLA-A9 molecule: HLA-A9.3.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1729171")) self.assertEqual(reference.references[1], ("DOI", "10.1007/bf00216625")) reference = record.references[9] self.assertEqual( reference.authors, "Madrigal J.A., Belich M.P., Hildebrand W.H., Benjamin R.J., Little A.-M., Zemmour J., Ennis P.D., Ward F.E., Petzl-Erler M.L., Martell R.W., du Toit E.D., Parham P.", ) self.assertEqual( reference.title, "Distinctive HLA-A,B antigens of black populations formed by interallelic conversion.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "1431115")) reference = record.references[10] self.assertEqual( reference.authors, "Belich M.P., Madrigal J.A., Hildebrand W.H., Zemmour J., Williams R.C., Luz R., Petzl-Erler M.L., Parham P.", ) self.assertEqual( reference.title, "Unusual HLA-B alleles in two tribes of Brazilian Indians." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1317015")) self.assertEqual(reference.references[1], ("DOI", "10.1038/357326a0")) reference = record.references[11] self.assertEqual( reference.authors, "Madrigal J.A., Hildebrand W.H., Belich M.P., Benjamin R.J., Little A.-M., Zemmour J., Ennis P.D., Ward F.E., Petzl-Erler M.L., du Toit E.D., Parham P.", ) self.assertEqual( reference.title, "Structural diversity in the HLA-A10 family of alleles: correlations with serology.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8475492")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1399-0039.1993.tb01982.x") ) reference = record.references[12] self.assertEqual( reference.authors, "Domena J.D., Hildebrand W.H., Bias W.B., Parham P." ) self.assertEqual( reference.title, "A sixth family of HLA-A alleles defined by HLA-A*8001." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8284791")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1399-0039.1993.tb02186.x") ) reference = record.references[13] self.assertEqual( reference.authors, "Ishikawa Y., Tokunaga K., Lin L., Imanishi T., Saitou S., Kashiwase K., Akaza T., Tadokoro K., Juji T.", ) self.assertEqual( reference.title, "Sequences of four splits of HLA-A10 group. Implications for serologic cross-reactivities and their evolution.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8026990")) self.assertEqual( reference.references[1], ("DOI", "10.1016/0198-8859(94)90263-1") ) reference = record.references[14] self.assertEqual( reference.authors, "Balas A., Garcia-Sanchez F., Gomez-Reino F., Vicario J.L.", ) self.assertEqual( reference.title, "Characterization of a new and highly distinguishable HLA-A allele in a Spanish family.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8188325")) self.assertEqual(reference.references[1], ("DOI", "10.1007/bf00176169")) reference = record.references[15] self.assertEqual( reference.authors, "Lin L., Tokunaga K., Ishikawa Y., Bannai M., Kashiwase K., Kuwata S., Akaza T., Tadokoro K., Shibata Y., Juji T.", ) self.assertEqual( reference.title, "Sequence analysis of serological HLA-A11 split antigens, A11.1 and A11.2.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8016845")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1399-0039.1994.tb02304.x") ) reference = record.references[16] self.assertEqual(reference.authors, "Olerup O., Daniels T.J., Baxter-Lowe L.") self.assertEqual( reference.title, "Correct sequence of the A*3001 allele obtained by PCR-SSP typing and automated nucleotide sequencing.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "7871528")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1399-0039.1994.tb02393.x") ) reference = record.references[17] self.assertEqual(reference.authors, "Sun Y., Liu S., Luo Y., Liang F., Xi Y.") self.assertEqual( reference.title, "Identification and frequency of a novel HLA-A allele, A*110104.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17092262")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1399-0039.2006.00687.x") ) reference = record.references[18] self.assertEqual( reference.authors, "Strachan T., Sodoyer R., Damotte M., Jordan B.R." ) self.assertEqual( reference.title, "Complete nucleotide sequence of a functional class I HLA gene, HLA-A3: implications for the evolution of HLA genes.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "6609814")) self.assertEqual( reference.references[1], ("DOI", "10.1002/j.1460-2075.1984.tb01901.x") ) reference = record.references[19] self.assertEqual(reference.authors, "Holmes N., Parham P.") self.assertEqual( reference.title, "Exon shuffling in vivo can generate novel HLA class I molecules.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "3877632")) self.assertEqual( reference.references[1], ("DOI", "10.1002/j.1460-2075.1985.tb04013.x") ) reference = record.references[20] self.assertEqual(reference.authors, "Koller B.H., Orr H.T.") self.assertEqual( reference.title, "Cloning and complete sequence of an HLA-A2 gene: analysis of two HLA-A alleles at the nucleotide level.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "2982951")) reference = record.references[21] self.assertEqual( reference.authors, "Cowan E.P., Jelachich M.L., Biddison W.E., Coligan J.E." ) self.assertEqual( reference.title, "DNA sequence of HLA-A11: remarkable homology with HLA-A3 allows identification of residues involved in epitopes recognized by antibodies and T cells.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2437024")) self.assertEqual(reference.references[1], ("DOI", "10.1007/bf00404694")) reference = record.references[22] self.assertEqual(reference.authors, "Girdlestone J.") self.assertEqual(reference.title, "Nucleotide sequence of an HLA-A1 gene.") self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2251137")) self.assertEqual(reference.references[1], ("DOI", "10.1093/nar/18.22.6701")) reference = record.references[23] self.assertEqual( reference.authors, "Balas A., Garcia-Sanchez F., Gomez-Reino F., Vicario J.L.", ) self.assertEqual( reference.title, "HLA class I allele (HLA-A2) expression defect associated with a mutation in its enhancer B inverted CAT box in two families.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "7836067")) self.assertEqual( reference.references[1], ("DOI", "10.1016/0198-8859(94)90087-6") ) reference = record.references[24] self.assertEqual(reference.authors, "Arnett K.L., Adams E.J., Parham P.") self.assertEqual(reference.title, "On the sequence of A*3101.") self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8795145")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1399-0039.1996.tb02580.x") ) reference = record.references[25] self.assertEqual( reference.authors, "Laforet M., Froelich N., Parissiadis A., Bausinger H., Pfeiffer B., Tongio M.M.", ) self.assertEqual( reference.title, "An intronic mutation responsible for a low level of expression of an HLA-A*24 allele.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "9349616")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1399-0039.1997.tb02884.x") ) reference = record.references[26] self.assertEqual( reference.authors, "Laforet M., Froelich N., Parissiadis A., Pfeiffer B., Schell A., Faller B., Woehl-Jaegle M.L., Cazenave J.-P., Tongio M.M.", ) self.assertEqual( reference.title, "A nucleotide insertion in exon 4 is responsible for the absence of expression of an HLA-A*01 allele.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "9349617")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1399-0039.1997.tb02885.x") ) reference = record.references[27] self.assertEqual( reference.authors, "Zhu F., He Y., Zhang W., He J., He J., Xu X., Yan L." ) self.assertEqual( reference.title, "Analysis of the complete genomic sequence of HLA-A alleles in the Chinese Han population.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19735485")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1744-313x.2009.00874.x") ) reference = record.references[28] self.assertEqual(reference.authors, "Domena J.D.") self.assertEqual(reference.title, "") self.assertEqual(len(reference.references), 0) reference = record.references[29] self.assertEqual(reference.authors, "Hurley C.K.") self.assertEqual(reference.title, "") self.assertEqual(len(reference.references), 0) reference = record.references[30] self.assertEqual(reference.authors, "Ellexson M.E., Hildebrand W.H.") self.assertEqual(reference.title, "") self.assertEqual(len(reference.references), 0) reference = record.references[31] self.assertEqual(reference.authors, "Mayor N.P.") self.assertEqual( reference.title, "Full length sequence of an HLA-A*0301 intron 2 variant." ) self.assertEqual(len(reference.references), 0) reference = record.references[32] self.assertEqual(reference.authors, "The MGC Project Team") self.assertEqual( reference.title, "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "15489334")) self.assertEqual(reference.references[1], ("DOI", "10.1101/gr.2596504")) reference = record.references[33] self.assertEqual( reference.authors, "Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D., Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.", ) self.assertEqual( reference.title, "The DNA sequence and analysis of human chromosome 6." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "14574404")) self.assertEqual(reference.references[1], ("DOI", "10.1038/nature02055")) reference = record.references[34] self.assertEqual( reference.authors, "Orr H.T., Lopez de Castro J.A., Parham P., Ploegh H.L., Strominger J.L.", ) self.assertEqual( reference.title, "Comparison of amino acid sequences of two human histocompatibility antigens, HLA-A2 and HLA-B7: location of putative alloantigenic sites.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "92029")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.76.9.4395")) reference = record.references[35] self.assertEqual( reference.authors, "Lopez de Castro J.A., Strominger J.L., Strong D.M., Orr H.T.", ) self.assertEqual( reference.title, "Structure of crossreactive human histocompatibility antigens HLA-A28 and HLA-A2: possible implications for the generation of HLA polymorphism.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "6179086")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.79.12.3813")) reference = record.references[36] self.assertEqual( reference.authors, "Jelachich M.L., Cowan E.P., Turner R.V., Coligan J.E., Biddison W.E.", ) self.assertEqual( reference.title, "Analysis of the molecular basis of HLA-A3 recognition by cytotoxic T cells using defined mutants of the HLA-A3 molecule.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "2456340")) reference = record.references[37] self.assertEqual( reference.authors, "Salter R.D., Norment A.M., Chen B.P., Clayberger C., Krensky A.M., Littman D.R., Parham P.", ) self.assertEqual( reference.title, "Polymorphism in the alpha 3 domain of HLA-A molecules affects binding to CD8.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2784196")) self.assertEqual(reference.references[1], ("DOI", "10.1038/338345a0")) reference = record.references[38] self.assertEqual( reference.authors, "Traversari C., van der Bruggen P., Luescher I.F., Lurquin C., Chomez P., Van Pel A., De Plaen E., Amar-Costesec A., Boon T.", ) self.assertEqual( reference.title, "A nonapeptide encoded by human gene MAGE-1 is recognized on HLA-A1 by cytolytic T lymphocytes directed against tumor antigen MZ2-E.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1402688")) self.assertEqual(reference.references[1], ("DOI", "10.1084/jem.176.5.1453")) reference = record.references[39] self.assertEqual( reference.authors, "DiBrino M., Tsuchida T., Turner R.V., Parker K.C., Coligan J.E., Biddison W.E.", ) self.assertEqual( reference.title, "HLA-A1 and HLA-A3 T cell epitopes derived from influenza virus proteins predicted from peptide binding motifs.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "7504010")) reference = record.references[40] self.assertEqual( reference.authors, "DiBrino M., Parker K.C., Shiloach J., Knierman M., Lukszo J., Turner R.V., Biddison W.E., Coligan J.E.", ) self.assertEqual( reference.title, "Endogenous peptides bound to HLA-A3 possess a specific combination of anchor residues that permit identification of potential antigenic peptides.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "7679507")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.90.4.1508")) reference = record.references[41] self.assertEqual( reference.authors, "DiBrino M., Parker K.C., Shiloach J., Turner R.V., Tsuchida T., Garfield M., Biddison W.E., Coligan J.E.", ) self.assertEqual( reference.title, "Endogenous peptides with distinct amino acid anchor residue motifs bind to HLA-A1 and HLA-B8.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "7506728")) reference = record.references[42] self.assertEqual( reference.authors, "Lewis J.W., Neisig A., Neefjes J., Elliott T." ) self.assertEqual( reference.title, "Point mutations in the alpha 2 domain of HLA-A2.1 define a functionally relevant interaction with TAP.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8805302")) self.assertEqual( reference.references[1], ("DOI", "10.1016/s0960-9822(02)00611-5") ) reference = record.references[43] self.assertEqual( reference.authors, "Peace-Brewer A.L., Tussey L.G., Matsui M., Li G., Quinn D.G., Frelinger J.A.", ) self.assertEqual( reference.title, "A point mutation in HLA-A*0201 results in failure to bind the TAP complex and to present virus-derived peptides to CTL.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8630735")) self.assertEqual( reference.references[1], ("DOI", "10.1016/s1074-7613(00)80416-1") ) reference = record.references[44] self.assertEqual( reference.authors, "Boisgerault F., Khalil I., Tieng V., Connan F., Tabary T., Cohen J.H., Choppin J., Charron D., Toubert A.", ) self.assertEqual( reference.title, "Definition of the HLA-A29 peptide ligand motif allows prediction of potential T-cell epitopes from the retinal soluble antigen, a candidate autoantigen in birdshot retinopathy.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8622959")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.93.8.3466")) reference = record.references[45] self.assertEqual( reference.authors, "Ikeda H., Lethe B.G., Lehmann F., van Baren N., Baurain J.-F., de Smet C., Chambost H., Vitale M., Moretta A., Boon T., Coulie P.G.", ) self.assertEqual( reference.title, "Characterization of an antigen that is recognized on a melanoma showing partial HLA loss by CTL expressing an NK inhibitory receptor.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "9047241")) self.assertEqual( reference.references[1], ("DOI", "10.1016/s1074-7613(00)80426-4") ) reference = record.references[46] self.assertEqual( reference.authors, "Kawakami Y., Robbins P.F., Wang X., Tupesis J.P., Parkhurst M.R., Kang X., Sakaguchi K., Appella E., Rosenberg S.A.", ) self.assertEqual( reference.title, "Identification of new melanoma epitopes on melanosomal proteins recognized by tumor infiltrating T lymphocytes restricted by HLA-A1, -A2, and -A3 alleles.", ) self.assertEqual(len(reference.references), 1) self.assertEqual(reference.references[0], ("PubMed", "9862734")) reference = record.references[47] self.assertEqual( reference.authors, "Fukada K., Chujoh Y., Tomiyama H., Miwa K., Kaneko Y., Oka S., Takiguchi M.", ) self.assertEqual( reference.title, "HLA-A*1101-restricted cytotoxic T lymphocyte recognition of HIV-1 Pol protein.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "10449296")) self.assertEqual( reference.references[1], ("DOI", "10.1097/00002030-199907300-00021") ) reference = record.references[48] self.assertEqual( reference.authors, "Johnson J.M., Nicot C., Fullen J., Ciminale V., Casareto L., Mulloy J.C., Jacobson S., Franchini G.", ) self.assertEqual( reference.title, "Free major histocompatibility complex class I heavy chain is preferentially targeted for degradation by human T-cell leukemia/lymphotropic virus type 1 p12(I) protein.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "11390610")) self.assertEqual( reference.references[1], ("DOI", "10.1128/jvi.75.13.6086-6094.2001") ) reference = record.references[49] self.assertEqual( reference.authors, "Hewitt E.W., Duncan L., Mufti D., Baker J., Stevenson P.G., Lehner P.J.", ) self.assertEqual( reference.title, "Ubiquitylation of MHC class I by the K3 viral protein signals internalization and TSG101-dependent degradation.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "12006494")) self.assertEqual(reference.references[1], ("DOI", "10.1093/emboj/21.10.2418")) reference = record.references[50] self.assertEqual( reference.authors, "Nagata Y., Ono S., Matsuo M., Gnjatic S., Valmori D., Ritter G., Garrett W., Old L.J., Mellman I.", ) self.assertEqual( reference.title, "Differential presentation of a soluble exogenous tumor antigen, NY-ESO-1, by distinct human dendritic cell populations.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "12138174")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.112331099")) reference = record.references[51] self.assertEqual( reference.authors, "Kuzushima K., Hayashi N., Kudoh A., Akatsuka Y., Tsujimura K., Morishima Y., Tsurumi T.", ) self.assertEqual( reference.title, "Tetramer-assisted identification and characterization of epitopes recognized by HLA A*2402-restricted Epstein-Barr virus-specific CD8+ T cells.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "12393434")) self.assertEqual(reference.references[1], ("DOI", "10.1182/blood-2002-04-1240")) reference = record.references[52] self.assertEqual( reference.authors, "Satoh M., Takamiya Y., Oka S., Tokunaga K., Takiguchi M.", ) self.assertEqual( reference.title, "Identification and characterization of HIV-1-specific CD8+ T cell epitopes presented by HLA-A*2601.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "15893615")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.vaccine.2005.02.022") ) reference = record.references[53] self.assertEqual( reference.authors, "Asemissen A.M., Keilholz U., Tenzer S., Mueller M., Walter S., Stevanovic S., Schild H., Letsch A., Thiel E., Rammensee H.G., Scheibenbogen C.", ) self.assertEqual( reference.title, "Identification of a highly immunogenic HLA-A*01-binding T cell epitope of WT1.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17189421")) self.assertEqual( reference.references[1], ("DOI", "10.1158/1078-0432.ccr-06-1337") ) reference = record.references[54] self.assertEqual( reference.authors, "Thananchai H., Gillespie G., Martin M.P., Bashirova A., Yawata N., Yawata M., Easterbrook P., McVicar D.W., Maenaka K., Parham P., Carrington M., Dong T., Rowland-Jones S.", ) self.assertEqual( reference.title, "Cutting Edge: Allele-specific and peptide-dependent interactions between KIR3DL1 and HLA-A and HLA-B.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17182537")) self.assertEqual(reference.references[1], ("DOI", "10.4049/jimmunol.178.1.33")) reference = record.references[55] self.assertEqual( reference.authors, "Robek M.D., Garcia M.L., Boyd B.S., Chisari F.V." ) self.assertEqual( reference.title, "Role of immunoproteasome catalytic subunits in the immune response to hepatitis B virus.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "17079320")) self.assertEqual(reference.references[1], ("DOI", "10.1128/jvi.01779-06")) reference = record.references[56] self.assertEqual( reference.authors, "Stern M., Ruggeri L., Capanni M., Mancusi A., Velardi A.", ) self.assertEqual( reference.title, "Human leukocyte antigens A23, A24, and A32 but not A25 are ligands for KIR3DL1.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "18502829")) self.assertEqual( reference.references[1], ("DOI", "10.1182/blood-2008-02-137521") ) reference = record.references[57] self.assertEqual(reference.authors, "Brennan R.M., Burrows S.R.") self.assertEqual( reference.title, "A mechanism for the HLA-A*01-associated risk for EBV+ Hodgkin lymphoma and infectious mononucleosis.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "18779413")) self.assertEqual( reference.references[1], ("DOI", "10.1182/blood-2008-06-162883") ) reference = record.references[58] self.assertEqual( reference.authors, "Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.", ) self.assertEqual( reference.title, "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19159218")) self.assertEqual(reference.references[1], ("DOI", "10.1021/pr8008012")) reference = record.references[59] self.assertEqual( reference.authors, "Hadrup S.R., Bakker A.H., Shu C.J., Andersen R.S., van Veluw J., Hombrink P., Castermans E., Thor Straten P., Blank C., Haanen J.B., Heemskerk M.H., Schumacher T.N.", ) self.assertEqual( reference.title, "Parallel detection of antigen-specific T-cell responses by multidimensional encoding of MHC multimers.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19543285")) self.assertEqual(reference.references[1], ("DOI", "10.1038/nmeth.1345")) reference = record.references[60] self.assertEqual( reference.authors, "Parmentier N., Stroobant V., Colau D., de Diesbach P., Morel S., Chapiro J., van Endert P., Van den Eynde B.J.", ) self.assertEqual( reference.title, "Production of an antigenic peptide by insulin-degrading enzyme.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "20364150")) self.assertEqual(reference.references[1], ("DOI", "10.1038/ni.1862")) reference = record.references[61] self.assertEqual( reference.authors, "Marsh S.G., Albert E.D., Bodmer W.F., Bontrop R.E., Dupont B., Erlich H.A., Fernandez-Vina M., Geraghty D.E., Holdsworth R., Hurley C.K., Lau M., Lee K.W., Mach B., Maiers M., Mayr W.R., Mueller C.R., Parham P., Petersdorf E.W., Sasazuki T., Strominger J.L., Svejgaard A., Terasaki P.I., Tiercy J.M., Trowsdale J.", ) self.assertEqual( reference.title, "Nomenclature for factors of the HLA system, 2010." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "20356336")) self.assertEqual( reference.references[1], ("DOI", "10.1111/j.1399-0039.2010.01466.x") ) reference = record.references[62] self.assertEqual( reference.authors, "Rizvi S.M., Del Cid N., Lybarger L., Raghavan M." ) self.assertEqual( reference.title, "Distinct functions for the glycans of tapasin and heavy chains in the assembly of MHC class I molecules.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21263072")) self.assertEqual(reference.references[1], ("DOI", "10.4049/jimmunol.1002959")) reference = record.references[63] self.assertEqual( reference.authors, "Matthews P.C., Adland E., Listgarten J., Leslie A., Mkhwanazi N., Carlson J.M., Harndahl M., Stryhn A., Payne R.P., Ogwu A., Huang K.H., Frater J., Paioni P., Kloverpris H., Jooste P., Goedhals D., van Vuuren C., Steyn D., Riddell L., Chen F., Luzzi G., Balachandran T., Ndung'u T., Buus S., Carrington M., Shapiro R., Heckerman D., Goulder P.J.", ) self.assertEqual( reference.title, "HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21498667")) self.assertEqual(reference.references[1], ("DOI", "10.4049/jimmunol.1003711")) reference = record.references[64] self.assertEqual( reference.authors, "Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J., Mohammed S.", ) self.assertEqual( reference.title, "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "23186163")) self.assertEqual(reference.references[1], ("DOI", "10.1021/pr300630k")) reference = record.references[65] self.assertEqual( reference.authors, "Shimizu A., Kawana-Tachikawa A., Yamagata A., Han C., Zhu D., Sato Y., Nakamura H., Koibuchi T., Carlson J., Martin E., Brumme C.J., Shi Y., Gao G.F., Brumme Z.L., Fukai S., Iwamoto A.", ) self.assertEqual( reference.title, "Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "24192765")) self.assertEqual(reference.references[1], ("DOI", "10.1038/srep03097")) reference = record.references[66] self.assertEqual( reference.authors, "Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.", ) self.assertEqual( reference.title, "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "24275569")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.jprot.2013.11.014") ) reference = record.references[67] self.assertEqual( reference.authors, "Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M., Ayoub D., Lane L., Bairoch A., Van Dorsselaer A., Carapito C.", ) self.assertEqual( reference.title, "N-terminome analysis of the human mitochondrial proteome." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "25944712")) self.assertEqual(reference.references[1], ("DOI", "10.1002/pmic.201400617")) reference = record.references[68] self.assertEqual( reference.authors, "Giam K., Ayala-Perez R., Illing P.T., Schittenhelm R.B., Croft N.P., Purcell A.W., Dudek N.L.", ) self.assertEqual( reference.title, "A comprehensive analysis of peptides presented by HLA-A1." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "25880248")) self.assertEqual(reference.references[1], ("DOI", "10.1111/tan.12565")) reference = record.references[69] self.assertEqual( reference.authors, "Morozov G.I., Zhao H., Mage M.G., Boyd L.F., Jiang J., Dolan M.A., Venna R., Norcross M.A., McMurtrey C.P., Hildebrand W., Schuck P., Natarajan K., Margulies D.H.", ) self.assertEqual( reference.title, "Interaction of TAPBPR, a tapasin homolog, with MHC-I molecules promotes peptide editing.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "26869717")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.1519894113")) reference = record.references[70] self.assertEqual( reference.authors, "Tripathi S.C., Peters H.L., Taguchi A., Katayama H., Wang H., Momin A., Jolly M.K., Celiktas M., Rodriguez-Canales J., Liu H., Behrens C., Wistuba I.I., Ben-Jacob E., Levine H., Molldrem J.J., Hanash S.M., Ostrin E.J.", ) self.assertEqual( reference.title, "Immunoproteasome deficiency is a feature of non-small cell lung cancer with a mesenchymal phenotype and is associated with a poor outcome.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "26929325")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.1521812113")) reference = record.references[71] self.assertEqual( reference.authors, "Ebstein F., Textoris-Taube K., Keller C., Golnik R., Vigneron N., Van den Eynde B.J., Schuler-Thurner B., Schadendorf D., Lorenz F.K., Uckert W., Urban S., Lehmann A., Albrecht-Koepke N., Janek K., Henklein P., Niewienda A., Kloetzel P.M., Mishto M.", ) self.assertEqual( reference.title, "Proteasomes generate spliced epitopes by two different mechanisms and as efficiently as non-spliced epitopes.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "27049119")) self.assertEqual(reference.references[1], ("DOI", "10.1038/srep24032")) reference = record.references[72] self.assertEqual( reference.authors, "Keib A., Mei Y.F., Cicin-Sain L., Busch D.H., Dennehy K.M.", ) self.assertEqual( reference.title, "Measuring Antiviral Capacity of T Cell Responses to Adenovirus.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "30530481")) self.assertEqual(reference.references[1], ("DOI", "10.4049/jimmunol.1801003")) reference = record.references[73] self.assertEqual( reference.authors, "Oxford Immunology Network Covid-19 Response T cell Consortium; ISARIC4C Investigators; Peng Y., Mentzer A.J., Liu G., Yao X., Yin Z., Dong D., Dejnirattisai W., Rostron T., Supasa P., Liu C., Lopez-Camacho C., Slon-Campos J., Zhao Y., Stuart D.I., Paesen G.C., Grimes J.M., Antson A.A., Bayfield O.W., Hawkins D.E.D.P., Ker D.S., Wang B., Turtle L., Subramaniam K., Thomson P., Zhang P., Dold C., Ratcliff J., Simmonds P., de Silva T., Sopp P., Wellington D., Rajapaksa U., Chen Y.L., Salio M., Napolitani G., Paes W., Borrow P., Kessler B.M., Fry J.W., Schwabe N.F., Semple M.G., Baillie J.K., Moore S.C., Openshaw P.J.M., Ansari M.A., Dunachie S., Barnes E., Frater J., Kerr G., Goulder P., Lockett T., Levin R., Zhang Y., Jing R., Ho L.P., Cornall R.J., Conlon C.P., Klenerman P., Screaton G.R., Mongkolsapaya J., McMichael A., Knight J.C., Ogg G., Dong T.", ) self.assertEqual( reference.title, "Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "32887977")) self.assertEqual(reference.references[1], ("DOI", "10.1038/s41590-020-0782-6")) reference = record.references[74] self.assertEqual( reference.authors, "Guo H.-C., Jardetzky T.S., Garrett T.P.J., Lane W.S., Strominger J.L., Wiley D.C.", ) self.assertEqual( reference.title, "Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1448153")) self.assertEqual(reference.references[1], ("DOI", "10.1038/360364a0")) reference = record.references[75] self.assertEqual( reference.authors, "Silver M.L., Guo H.-C., Strominger J.L., Wiley D.C." ) self.assertEqual( reference.title, "Atomic structure of a human MHC molecule presenting an influenza virus peptide.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1448154")) self.assertEqual(reference.references[1], ("DOI", "10.1038/360367a0")) reference = record.references[76] self.assertEqual(reference.authors, "Madden D.R., Garboczi D.N., Wiley D.C.") self.assertEqual( reference.title, "The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "7694806")) self.assertEqual( reference.references[1], ("DOI", "10.1016/0092-8674(93)90490-h") ) reference = record.references[77] self.assertEqual(reference.authors, "Collins E.J., Garboczi D.N., Wiley D.C.") self.assertEqual( reference.title, "Three-dimensional structure of a peptide extending from one end of a class I MHC binding site.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "7935798")) self.assertEqual(reference.references[1], ("DOI", "10.1038/371626a0")) reference = record.references[78] self.assertEqual( reference.authors, "Garboczi D.N., Ghosh P., Utz U., Fan Q.R., Biddison W.E., Wiley D.C.", ) self.assertEqual( reference.title, "Structure of the complex between human T-cell receptor, viral peptide and HLA-A2.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "8906788")) self.assertEqual(reference.references[1], ("DOI", "10.1038/384134a0")) reference = record.references[79] self.assertEqual( reference.authors, "Gao G.F., Tormo J., Gerth U.C., Wyer J.R., McMichael A.J., Stuart D.I., Bell J.I., Jones E.Y., Jakobsen B.K.", ) self.assertEqual( reference.title, "Crystal structure of the complex between human CD8alpha(alpha) and HLA-A2.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "9177355")) self.assertEqual(reference.references[1], ("DOI", "10.1038/42523")) reference = record.references[80] self.assertEqual( reference.authors, "Hillig R.C., Coulie P.G., Stroobant V., Saenger W., Ziegler A., Hulsmeyer M.", ) self.assertEqual( reference.title, "High-resolution structure of HLA-A*0201 in complex with a tumour-specific antigenic peptide encoded by the MAGE-A4 gene.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "11502003")) self.assertEqual(reference.references[1], ("DOI", "10.1006/jmbi.2001.4816")) reference = record.references[81] self.assertEqual( reference.authors, "Stewart-Jones G.B.E., McMichael A.J., Bell J.I., Stuart D.I., Jones E.Y.", ) self.assertEqual( reference.title, "A structural basis for immunodominant human T cell receptor recognition.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "12796775")) self.assertEqual(reference.references[1], ("DOI", "10.1038/ni942")) reference = record.references[82] self.assertEqual( reference.authors, "Blicher T., Kastrup J.S., Buus S., Gajhede M." ) self.assertEqual( reference.title, "High-resolution structure of HLA-A*1101 in complex with SARS nucleocapsid peptide.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "16041067")) self.assertEqual(reference.references[1], ("DOI", "10.1107/s0907444905013090")) reference = record.references[83] self.assertEqual( reference.authors, "Ishizuka J., Stewart-Jones G.B., van der Merwe A., Bell J.I., McMichael A.J., Jones E.Y.", ) self.assertEqual( reference.title, "The structural dynamics and energetics of an immunodominant T cell receptor are programmed by its Vbeta domain.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "18275829")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.immuni.2007.12.018") ) reference = record.references[84] self.assertEqual( reference.authors, "Gras S., Saulquin X., Reiser J.B., Debeaupuis E., Echasserieau K., Kissenpfennig A., Legoux F., Chouquet A., Le Gorrec M., Machillot P., Neveu B., Thielens N., Malissen B., Bonneville M., Housset D.", ) self.assertEqual( reference.title, "Structural bases for the affinity-driven selection of a public TCR against a dominant human cytomegalovirus epitope.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19542454")) self.assertEqual(reference.references[1], ("DOI", "10.4049/jimmunol.0900556")) reference = record.references[85] self.assertEqual( reference.authors, "Kumar P., Vahedi-Faridi A., Saenger W., Ziegler A., Uchanska-Ziegler B.", ) self.assertEqual( reference.title, "Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "19177349")) self.assertEqual(reference.references[1], ("DOI", "10.1002/pro.4")) reference = record.references[86] self.assertEqual( reference.authors, "Liu J., Wu P., Gao F., Qi J., Kawana-Tachikawa A., Xie J., Vavricka C.J., Iwamoto A., Li T., Gao G.F.", ) self.assertEqual( reference.title, "Novel immunodominant peptide presentation strategy: a featured HLA-A*2402-restricted cytotoxic T-lymphocyte epitope stabilized by intrachain hydrogen bonds from severe acute respiratory syndrome coronavirus nucleocapsid protein.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "20844028")) self.assertEqual(reference.references[1], ("DOI", "10.1128/jvi.01464-10")) reference = record.references[87] self.assertEqual(reference.authors, "Borbulevych O.Y., Do P., Baker B.M.") self.assertEqual( reference.title, "Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: implications for WT1-based cancer therapeutics.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "20619457")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.molimm.2010.06.005") ) reference = record.references[88] self.assertEqual( reference.authors, "McMahon R.M., Friis L., Siebold C., Friese M.A., Fugger L., Jones E.Y.", ) self.assertEqual( reference.title, "Structure of HLA-A*0301 in complex with a peptide of proteolipid protein: insights into the role of HLA-A alleles in susceptibility to multiple sclerosis.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21543847")) self.assertEqual(reference.references[1], ("DOI", "10.1107/s0907444911007888")) reference = record.references[89] self.assertEqual( reference.authors, "Zhang S., Liu J., Cheng H., Tan S., Qi J., Yan J., Gao G.F.", ) self.assertEqual( reference.title, "Structural basis of cross-allele presentation by HLA-A*0301 and HLA-A*1101 revealed by two HIV-derived peptide complexes.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21943705")) self.assertEqual( reference.references[1], ("DOI", "10.1016/j.molimm.2011.08.015") ) reference = record.references[90] self.assertEqual( reference.authors, "Bulek A.M., Cole D.K., Skowera A., Dolton G., Gras S., Madura F., Fuller A., Miles J.J., Gostick E., Price D.A., Drijfhout J.W., Knight R.R., Huang G.C., Lissin N., Molloy P.E., Wooldridge L., Jakobsen B.K., Rossjohn J., Peakman M., Rizkallah P.J., Sewell A.K.", ) self.assertEqual( reference.title, "Structural basis for the killing of human beta cells by CD8(+) T cells in type 1 diabetes.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "22245737")) self.assertEqual(reference.references[1], ("DOI", "10.1038/ni.2206")) reference = record.references[91] self.assertEqual( reference.authors, "Quinones-Parra S., Grant E., Loh L., Nguyen T.H., Campbell K.A., Tong S.Y., Miller A., Doherty P.C., Vijaykrishna D., Rossjohn J., Gras S., Kedzierska K.", ) self.assertEqual( reference.title, "Preexisting CD8+ T-cell immunity to the H7N9 influenza A virus varies across ethnicities.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "24395804")) self.assertEqual(reference.references[1], ("DOI", "10.1073/pnas.1322229111")) reference = record.references[92] self.assertEqual( reference.authors, "Raman M.C., Rizkallah P.J., Simmons R., Donnellan Z., Dukes J., Bossi G., Le Provost G.S., Todorov P., Baston E., Hickman E., Mahon T., Hassan N., Vuidepot A., Sami M., Cole D.K., Jakobsen B.K.", ) self.assertEqual( reference.title, "Direct molecular mimicry enables off-target cardiovascular toxicity by an enhanced affinity TCR designed for cancer immunotherapy.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "26758806")) self.assertEqual(reference.references[1], ("DOI", "10.1038/srep18851")) reference = record.references[93] self.assertEqual( reference.authors, "Song I., Gil A., Mishra R., Ghersi D., Selin L.K., Stern L.J.", ) self.assertEqual( reference.title, "Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "28250417")) self.assertEqual(reference.references[1], ("DOI", "10.1038/nsmb.3383")) reference = record.references[94] self.assertEqual( reference.authors, "LeHoang P., Ozdemir N., Benhamou A., Tabary T., Edelson C., Betuel H., Semiglia R., Cohen J.H.", ) self.assertEqual( reference.title, "HLA-A29.2 subtype associated with birdshot retinochoroidopathy.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1728143")) self.assertEqual( reference.references[1], ("DOI", "10.1016/s0002-9394(14)75749-6") ) reference = record.references[95] self.assertEqual( reference.authors, "Fogdell-Hahn A., Ligers A., Groenning M., Hillert J., Olerup O.", ) self.assertEqual( reference.title, "Multiple sclerosis: a modifying influence of HLA class I genes in an HLA class II associated autoimmune disease.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "10746785")) self.assertEqual( reference.references[1], ("DOI", "10.1034/j.1399-0039.2000.550205.x") ) reference = record.references[96] self.assertEqual(reference.authors, "Nakanishi K., Inoko H.") self.assertEqual( reference.title, "Combination of HLA-A24, -DQA1*03, and -DR9 contributes to acute-onset and early complete beta-cell destruction in type 1 diabetes: longitudinal study of residual beta-cell function.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "16731854")) self.assertEqual(reference.references[1], ("DOI", "10.2337/db05-1049")) reference = record.references[97] self.assertEqual( reference.authors, "Skowera A., Ellis R.J., Varela-Calvino R., Arif S., Huang G.C., Van-Krinks C., Zaremba A., Rackham C., Allen J.S., Tree T.I., Zhao M., Dayan C.M., Sewell A.K., Unger W.W., Unger W., Drijfhout J.W., Ossendorp F., Roep B.O., Peakman M.", ) self.assertEqual( reference.title, "CTLs are targeted to kill beta cells in patients with type 1 diabetes through recognition of a glucose-regulated preproinsulin epitope.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "18802479")) self.assertEqual(reference.references[1], ("DOI", "10.1172/jci35449")) reference = record.references[98] self.assertEqual( reference.authors, "Friese M.A., Jakobsen K.B., Friis L., Etzensperger R., Craner M.J., McMahon R.M., Jensen L.T., Huygelen V., Jones E.Y., Bell J.I., Fugger L.", ) self.assertEqual( reference.title, "Opposing effects of HLA class I molecules in tuning autoreactive CD8+ T cells in multiple sclerosis.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "18953350")) self.assertEqual(reference.references[1], ("DOI", "10.1038/nm.1881")) reference = record.references[99] self.assertEqual( reference.authors, "Kronenberg D., Knight R.R., Estorninho M., Ellis R.J., Kester M.G., de Ru A., Eichmann M., Huang G.C., Powrie J., Dayan C.M., Skowera A., van Veelen P.A., Peakman M.", ) self.assertEqual( reference.title, "Circulating preproinsulin signal peptide-specific CD8 T cells restricted by the susceptibility molecule HLA-A24 are expanded at onset of type 1 diabetes and kill beta-cells.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "22522618")) self.assertEqual(reference.references[1], ("DOI", "10.2337/db11-1520")) reference = record.references[100] self.assertEqual( reference.authors, "McCormack M., Alfirevic A., Bourgeois S., Farrell J.J., Kasperaviciute D., Carrington M., Sills G.J., Marson T., Jia X., de Bakker P.I., Chinthapalli K., Molokhia M., Johnson M.R., O'Connor G.D., Chaila E., Alhusaini S., Shianna K.V., Radtke R.A., Heinzen E.L., Walley N., Pandolfo M., Pichler W., Park B.K., Depondt C., Sisodiya S.M., Goldstein D.B., Deloukas P., Delanty N., Cavalleri G.L., Pirmohamed M.", ) self.assertEqual( reference.title, "HLA-A*3101 and carbamazepine-induced hypersensitivity reactions in Europeans.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "21428769")) self.assertEqual(reference.references[1], ("DOI", "10.1056/nejmoa1013297")) reference = record.references[101] self.assertEqual( reference.authors, "Nakamura J., Meguro A., Ishii G., Mihara T., Takeuchi M., Mizuki Y., Yuda K., Yamane T., Kawagoe T., Ota M., Mizuki N.", ) self.assertEqual( reference.title, "The association analysis between HLA-A*26 and Behcet's disease.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "30872678")) self.assertEqual(reference.references[1], ("DOI", "10.1038/s41598-019-40824-y")) reference = record.references[102] self.assertEqual( reference.authors, "Robinson J., Guethlein L.A., Cereb N., Yang S.Y., Norman P.J., Marsh S.G.E., Parham P.", ) self.assertEqual( reference.title, "Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "28650991")) self.assertEqual( reference.references[1], ("DOI", "10.1371/journal.pgen.1006862") ) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_O23729(self): """Parsing SwissProt file O23729.txt.""" filename = "O23729.txt" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "O23729") self.assertEqual(seq_record.name, "CHS3_BROFI") self.assertEqual( seq_record.description, "RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Full=Naringenin-chalcone synthase 3;", ) self.assertEqual( repr(seq_record.seq), "Seq('MAPAMEEIRQAQRAEGPAAVLAIGTSTPPNALYQADYPDYYFRITKSEHLTELK...GAE')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "CHS3_BROFI") self.assertEqual(record.accessions, ["O23729"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Viridiplantae", "Streptophyta", "Embryophyta", "Tracheophyta", "Spermatophyta", "Magnoliopsida", "Liliopsida", "Asparagales", "Orchidaceae", "Epidendroideae", "Vandeae", "Adrorhizinae", "Bromheadia", ], ) self.assertEqual(record.seqinfo, (394, 42942, "2F8D14AF4870BBB2")) self.assertEqual(len(record.features), 2) feature = record.features[0] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 394) self.assertEqual(feature.qualifiers["note"], "Chalcone synthase 3") self.assertEqual(feature.id, "PRO_0000215956") feature = record.features[1] self.assertEqual(feature.type, "ACT_SITE") self.assertEqual(feature.location.start, 164) self.assertEqual(feature.location.end, 165) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|PROSITE-ProRule:PRU10023" ) self.assertIsNone(feature.id) self.assertEqual(len(record.references), 1) self.assertEqual( record.references[0].authors, "Liew C.F., Lim S.H., Loh C.S., Goh C.J." ) self.assertEqual( record.references[0].title, "Molecular cloning and sequence analysis of chalcone synthase cDNAs of Bromheadia finlaysoniana.", ) self.assertEqual(len(record.references[0].references), 0) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_Q13639(self): """Parsing SwissProt file Q13639.""" filename = "Q13639.txt" datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "Q13639") self.assertEqual(seq_record.name, "5HT4R_HUMAN") self.assertEqual( seq_record.description, "RecName: Full=5-hydroxytryptamine receptor 4; Short=5-HT-4; Short=5-HT4; AltName: Full=Serotonin receptor 4;", ) self.assertEqual( repr(seq_record.seq), "Seq('MDKLDANVSSEEGFGSVEKVVLLTFLSTVILMAILGNLLVMVAVCWDRQLRKIK...SDT')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "5HT4R_HUMAN") self.assertEqual( record.accessions, [ "Q13639", "Q96KH9", "Q96KI0", "Q9H199", "Q9NY73", "Q9UBM6", "Q9UBT4", "Q9UE22", "Q9UE23", "Q9UQR6", ], ) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Euarchontoglires", "Primates", "Haplorrhini", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (388, 43761, "7FCFEC60E7BDF560")) self.assertEqual(len(record.features), 26) feature = record.features[0] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 388) self.assertEqual( feature.qualifiers["description"], "5-hydroxytryptamine receptor 4." ) self.assertEqual(feature.id, "PRO_0000068965") feature = record.features[1] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 19) self.assertEqual( feature.qualifiers["description"], "Extracellular (By similarity)." ) self.assertIsNone(feature.id) feature = record.features[2] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 19) self.assertEqual(feature.location.end, 40) self.assertEqual(feature.qualifiers["description"], "1 (By similarity).") self.assertIsNone(feature.id) feature = record.features[3] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 40) self.assertEqual(feature.location.end, 58) self.assertEqual( feature.qualifiers["description"], "Cytoplasmic (By similarity)." ) self.assertIsNone(feature.id) feature = record.features[4] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 58) self.assertEqual(feature.location.end, 79) self.assertEqual(feature.qualifiers["description"], "2 (By similarity).") self.assertIsNone(feature.id) feature = record.features[5] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 79) self.assertEqual(feature.location.end, 93) self.assertEqual( feature.qualifiers["description"], "Extracellular (By similarity)." ) self.assertIsNone(feature.id) feature = record.features[6] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 93) self.assertEqual(feature.location.end, 116) self.assertEqual(feature.qualifiers["description"], "3 (By similarity).") self.assertIsNone(feature.id) feature = record.features[7] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 116) self.assertEqual(feature.location.end, 137) self.assertEqual( feature.qualifiers["description"], "Cytoplasmic (By similarity)." ) self.assertIsNone(feature.id) feature = record.features[8] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 137) self.assertEqual(feature.location.end, 158) self.assertEqual(feature.qualifiers["description"], "4 (By similarity).") self.assertIsNone(feature.id) feature = record.features[9] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 158) self.assertEqual(feature.location.end, 192) self.assertEqual( feature.qualifiers["description"], "Extracellular (By similarity)." ) self.assertIsNone(feature.id) feature = record.features[10] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 192) self.assertEqual(feature.location.end, 213) self.assertEqual(feature.qualifiers["description"], "5 (By similarity).") self.assertIsNone(feature.id) feature = record.features[11] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 213) self.assertEqual(feature.location.end, 260) self.assertEqual( feature.qualifiers["description"], "Cytoplasmic (By similarity)." ) self.assertIsNone(feature.id) feature = record.features[12] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 260) self.assertEqual(feature.location.end, 281) self.assertEqual(feature.qualifiers["description"], "6 (By similarity).") self.assertIsNone(feature.id) feature = record.features[13] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 281) self.assertEqual(feature.location.end, 294) self.assertEqual( feature.qualifiers["description"], "Extracellular (By similarity)." ) self.assertIsNone(feature.id) feature = record.features[14] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 294) self.assertEqual(feature.location.end, 315) self.assertEqual(feature.qualifiers["description"], "7 (By similarity).") self.assertIsNone(feature.id) feature = record.features[15] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 315) self.assertEqual(feature.location.end, 388) self.assertEqual( feature.qualifiers["description"], "Cytoplasmic (By similarity)." ) self.assertIsNone(feature.id) feature = record.features[16] self.assertEqual(feature.type, "LIPID") self.assertEqual(feature.location.start, 328) self.assertEqual(feature.location.end, 329) self.assertEqual( feature.qualifiers["description"], "S-palmitoyl cysteine (By similarity)." ) self.assertIsNone(feature.id) feature = record.features[17] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 6) self.assertEqual(feature.location.end, 7) self.assertEqual( feature.qualifiers["description"], "N-linked (GlcNAc...) (Potential)." ) self.assertIsNone(feature.id) feature = record.features[18] self.assertEqual(feature.type, "DISULFID") self.assertEqual(feature.location.start, 92) self.assertEqual(feature.location.end, 184) self.assertEqual(feature.qualifiers["description"], "By similarity.") self.assertIsNone(feature.id) feature = record.features[19] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 168) self.assertEqual(feature.location.end, 169) self.assertEqual( feature.qualifiers["description"], "L -> LERSLNQGLGQDFHA (in isoform 5-HT4(F)).", ) self.assertEqual(feature.id, "VSP_001845") feature = record.features[20] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 358) self.assertEqual(feature.location.end, 388) self.assertEqual( feature.qualifiers["description"], "RDAVECGGQWESQCHPPATSPLVAAQPSDT -> SSGTETDRRNFGIRKRRLTKPS (in isoform 5-HT4(D)).", ) self.assertEqual(feature.id, "VSP_001847") feature = record.features[21] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 358) self.assertEqual(feature.location.end, 388) self.assertEqual( feature.qualifiers["description"], "RDAVECGGQWESQCHPPATSPLVAAQPSDT -> SGCSPVSSFLLLFCNRPVPV (in isoform 5-HT4(E)).", ) self.assertEqual(feature.id, "VSP_001846") feature = record.features[22] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 359) self.assertEqual(feature.location.end, 388) self.assertEqual( feature.qualifiers["description"], "DAVECGGQWESQCHPPATSPLVAAQPSDT -> YTVLHRGHHQELEKLPIHNDPESLESCF (in isoform 5-HT4(A)).", ) self.assertEqual(feature.id, "VSP_001849") feature = record.features[23] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 359) self.assertEqual(feature.location.end, 388) self.assertEqual( feature.qualifiers["description"], "DAVECGGQWESQCHPPATSPLVAAQPSDT -> F (in isoform 5-HT4(C)).", ) self.assertEqual(feature.id, "VSP_001848") feature = record.features[24] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 359) self.assertEqual(feature.location.end, 388) self.assertEqual( feature.qualifiers["description"], "Missing (in isoform 5-HT4(G))." ) self.assertEqual(feature.id, "VSP_001850") feature = record.features[25] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 371) self.assertEqual(feature.location.end, 372) self.assertEqual( feature.qualifiers["description"], "C -> Y (in dbSNP:rs34826744)." ) self.assertEqual(feature.id, "VAR_049364") self.assertEqual(len(record.references), 8) self.assertEqual( record.references[0].authors, "Blondel O., Gastineau M., Dahmoune Y., Langlois M., Fischmeister R.", ) self.assertEqual( record.references[0].title, "Cloning, expression, and pharmacology of four human 5-hydroxytryptamine 4 receptor isoforms produced by alternative splicing in the carboxyl terminus.", ) self.assertEqual(len(record.references[0].references), 2) self.assertEqual(record.references[0].references[0], ("MEDLINE", "98264328")) self.assertEqual(record.references[0].references[1], ("PubMed", "9603189")) self.assertEqual( record.references[1].authors, "Van den Wyngaert I., Gommeren W., Jurzak M., Verhasselt P., Gordon R., Leysen J., Luyten W., Bender E.", ) self.assertEqual( record.references[1].title, "Cloning and expression of 5-HT4 receptor species and splice variants.", ) self.assertEqual(len(record.references[1].references), 0) self.assertEqual( record.references[2].authors, "Claeysen S., Faye P., Sebben M., Lemaire S., Bockaert J., Dumuis A.", ) self.assertEqual( record.references[2].title, "Cloning and expression of human 5-HT4S receptors. Effect of receptor density on their coupling to adenylyl cyclase.", ) self.assertEqual(len(record.references[2].references), 2) self.assertEqual(record.references[2].references[0], ("MEDLINE", "98012006")) self.assertEqual(record.references[2].references[1], ("PubMed", "9351641")) self.assertEqual( record.references[3].authors, "Claeysen S., Sebben M., Becamel C., Bockaert J., Dumuis A.", ) self.assertEqual( record.references[3].title, "Novel brain-specific 5-HT4 receptor splice variants show marked constitutive activity: role of the C-terminal intracellular domain.", ) self.assertEqual(len(record.references[3].references), 2) self.assertEqual(record.references[3].references[0], ("MEDLINE", "99238795")) self.assertEqual(record.references[3].references[1], ("PubMed", "10220570")) self.assertEqual( record.references[4].authors, "Vilaro M.T., Domenech T., Palacios J.M., Mengod G.", ) self.assertEqual( record.references[4].title, "Cloning and characterization of multiple human 5-HT4 receptor variants including a novel variant that lacks the alternatively spliced C-terminal exon.", ) self.assertEqual( record.references[4].location, "Submitted (SEP-2000) to the EMBL/GenBank/DDBJ databases.", ) self.assertEqual(len(record.references[4].comments), 1) self.assertEqual(record.references[4].comments[0], ("TISSUE", "Hippocampus")) self.assertEqual(len(record.references[4].positions), 1) self.assertEqual( record.references[4].positions[0], "NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 5-HT4(A); 5-HT4(E) AND 5-HT4(G)).", ) self.assertEqual(len(record.references[4].references), 0) self.assertEqual(len(record.references[5].positions), 1) self.assertEqual( record.references[5].positions[0], "NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 5-HT4(B)).", ) self.assertEqual(len(record.references[5].references), 2) self.assertEqual(record.references[5].references[0], ("PubMed", "15489334")) self.assertEqual( record.references[5].references[1], ("DOI", "10.1101/gr.2596504") ) self.assertEqual(record.references[5].authors, "The MGC Project Team") self.assertEqual( record.references[5].title, "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).", ) self.assertEqual( record.references[5].location, "Genome Res. 14:2121-2127(2004)." ) self.assertEqual( record.references[6].authors, "Bender E., Pindon A., van Oers I., Zhang Y.B., Gommeren W., Verhasselt P., Jurzak M., Leysen J., Luyten W.", ) self.assertEqual( record.references[6].title, "Structure of the human serotonin 5-HT4 receptor gene and cloning of a novel 5-HT4 splice variant.", ) self.assertEqual(len(record.references[6].references), 3) self.assertEqual(record.references[6].references[0], ("MEDLINE", "20110418")) self.assertEqual(record.references[6].references[1], ("PubMed", "10646498")) self.assertEqual( record.references[6].references[2], ("DOI", "10.1046/j.1471-4159.2000.740478.x"), ) self.assertEqual( record.references[7].authors, "Ullmer C., Schmuck K., Kalkman H.O., Luebbert H.", ) self.assertEqual( record.references[7].title, "Expression of serotonin receptor mRNAs in blood vessels.", ) self.assertEqual(len(record.references[7].references), 3) self.assertEqual(record.references[7].references[0], ("MEDLINE", "95385798")) self.assertEqual(record.references[7].references[1], ("PubMed", "7656980")) self.assertEqual( record.references[7].references[2], ("DOI", "10.1016/0014-5793(95)00828-W") ) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser records = list(SeqIO.parse(datafile, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_P16235(self): """Parsing SwissProt file P16235.txt.""" filename = "P16235.txt" # test the record parser datafile = os.path.join("SwissProt", filename) seq_record = SeqIO.read(datafile, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "P16235") self.assertEqual(seq_record.name, "LSHR_RAT") self.assertEqual( seq_record.description, "RecName: Full=Lutropin-choriogonadotropic hormone receptor; Short=LH/CG-R; AltName: Full=Luteinizing hormone receptor; Short=LSH-R; Flags: Precursor;", ) self.assertEqual( repr(seq_record.seq), "Seq('MGRRVPALRQLLVLAVLLLKPSQLQSRELSGSRCPEPCDCAPDGALRCPGPRAG...LTH')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "LSHR_RAT") self.assertEqual( record.accessions, ["P16235", "P70646", "Q63807", "Q63808", "Q63809", "Q6LDI7"], ) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Euarchontoglires", "Glires", "Rodentia", "Myomorpha", "Muroidea", "Muridae", "Murinae", "Rattus", ], ) self.assertEqual(record.seqinfo, (700, 78036, "31807E73BAC94F1F")) self.assertEqual(len(record.features), 56) feature = record.features[0] self.assertEqual(feature.type, "SIGNAL") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 26) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000269|PubMed:2601325,ECO:0000269|PubMed:2925659", ) feature = record.features[1] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 26) self.assertEqual(feature.location.end, 700) self.assertEqual( feature.qualifiers["note"], "Lutropin-choriogonadotropic hormone receptor" ) feature = record.features[2] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 26) self.assertEqual(feature.location.end, 362) self.assertEqual(feature.qualifiers["note"], "Extracellular") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[3] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 362) self.assertEqual(feature.location.end, 390) self.assertEqual(feature.qualifiers["note"], "Helical; Name=1") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[4] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 390) self.assertEqual(feature.location.end, 399) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[5] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 399) self.assertEqual(feature.location.end, 422) self.assertEqual(feature.qualifiers["note"], "Helical; Name=2") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[6] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 422) self.assertEqual(feature.location.end, 443) self.assertEqual(feature.qualifiers["note"], "Extracellular") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[7] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 443) self.assertEqual(feature.location.end, 466) self.assertEqual(feature.qualifiers["note"], "Helical; Name=3") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[8] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 466) self.assertEqual(feature.location.end, 486) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[9] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 486) self.assertEqual(feature.location.end, 509) self.assertEqual(feature.qualifiers["note"], "Helical; Name=4") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[10] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 509) self.assertEqual(feature.location.end, 529) self.assertEqual(feature.qualifiers["note"], "Extracellular") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[11] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 529) self.assertEqual(feature.location.end, 551) self.assertEqual(feature.qualifiers["note"], "Helical; Name=5") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[12] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 551) self.assertEqual(feature.location.end, 574) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[13] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 574) self.assertEqual(feature.location.end, 598) self.assertEqual(feature.qualifiers["note"], "Helical; Name=6") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[14] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 598) self.assertEqual(feature.location.end, 609) self.assertEqual(feature.qualifiers["note"], "Extracellular") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[15] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 609) self.assertEqual(feature.location.end, 631) self.assertEqual(feature.qualifiers["note"], "Helical; Name=7") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[16] self.assertEqual(feature.type, "TOPO_DOM") self.assertEqual(feature.location.start, 631) self.assertEqual(feature.location.end, 700) self.assertEqual(feature.qualifiers["note"], "Cytoplasmic") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[17] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 125) self.assertEqual(feature.location.end, 150) self.assertEqual(feature.qualifiers["note"], "LRR 1") feature = record.features[18] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 151) self.assertEqual(feature.location.end, 175) self.assertEqual(feature.qualifiers["note"], "LRR 2") feature = record.features[19] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 200) self.assertEqual(feature.qualifiers["note"], "LRR 3") feature = record.features[20] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 201) self.assertEqual(feature.location.end, 224) self.assertEqual(feature.qualifiers["note"], "LRR 4") feature = record.features[21] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 224) self.assertEqual(feature.location.end, 248) self.assertEqual(feature.qualifiers["note"], "LRR 5") feature = record.features[22] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 249) self.assertEqual(feature.location.end, 271) self.assertEqual(feature.qualifiers["note"], "LRR 6") feature = record.features[23] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 334) self.assertEqual(feature.location.end, 335) self.assertEqual(feature.qualifiers["note"], "Sulfotyrosine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000250|UniProtKB:P22888") feature = record.features[24] self.assertEqual(feature.type, "LIPID") self.assertEqual(feature.location.start, 646) self.assertEqual(feature.location.end, 647) self.assertEqual(feature.qualifiers["note"], "S-palmitoyl cysteine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305|PubMed:7776964") feature = record.features[25] self.assertEqual(feature.type, "LIPID") self.assertEqual(feature.location.start, 647) self.assertEqual(feature.location.end, 648) self.assertEqual(feature.qualifiers["note"], "S-palmitoyl cysteine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305|PubMed:7776964") feature = record.features[26] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 102) self.assertEqual(feature.location.end, 103) self.assertEqual(feature.qualifiers["note"], "N-linked (GlcNAc...) asparagine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[27] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 177) self.assertEqual(feature.location.end, 178) self.assertEqual(feature.qualifiers["note"], "N-linked (GlcNAc...) asparagine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[28] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 198) self.assertEqual(feature.location.end, 199) self.assertEqual(feature.qualifiers["note"], "N-linked (GlcNAc...) asparagine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[29] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 294) self.assertEqual(feature.location.end, 295) self.assertEqual(feature.qualifiers["note"], "N-linked (GlcNAc...) asparagine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[30] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 302) self.assertEqual(feature.location.end, 303) self.assertEqual(feature.qualifiers["note"], "N-linked (GlcNAc...) asparagine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[31] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 316) self.assertEqual(feature.location.end, 317) self.assertEqual(feature.qualifiers["note"], "N-linked (GlcNAc...) asparagine") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000255") feature = record.features[32] self.assertEqual(feature.type, "DISULFID") self.assertEqual(feature.location.start, 442) self.assertEqual(feature.location.end, 518) self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|PROSITE-ProRule:PRU00521" ) feature = record.features[33] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 82) self.assertEqual(feature.location.end, 132) self.assertEqual(feature.qualifiers["note"], "Missing (in isoform 1950)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[34] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 132) self.assertEqual(feature.location.end, 157) self.assertEqual(feature.qualifiers["note"], "Missing (in isoform 1759)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[35] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 183) self.assertEqual(feature.location.end, 700) self.assertEqual(feature.qualifiers["note"], "Missing (in isoform C2)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[36] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 231) self.assertEqual(feature.location.end, 293) self.assertEqual( feature.qualifiers["note"], "Missing (in isoform EA2, isoform EB and isoform B1)", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[37] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 231) self.assertEqual(feature.location.end, 251) self.assertEqual( feature.qualifiers["note"], "DISSTKLQALPSHGLESIQT -> PCRATGWSPFRRSSPCLPTH (in isoform 2075)", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[38] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 251) self.assertEqual(feature.location.end, 700) self.assertEqual(feature.qualifiers["note"], "Missing (in isoform 2075)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[39] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 293) self.assertEqual(feature.location.end, 367) self.assertEqual( feature.qualifiers["note"], "QNFSFSIFENFSKQCESTVRKADNETLYSAIFEENELSGWDYDYGFCSPKTLQCAPEPDAFNPCEDIMGYAFLR -> IFHFPFLKTSPNNAKAQLEKQITRRFIPPSLRRMNSVAGIMIMASVHPRHSNVLQNQMLSTPVKILWAMPSLGS (in isoform B1 and isoform B3)", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[40] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 293) self.assertEqual(feature.location.end, 294) self.assertEqual(feature.qualifiers["note"], "Q -> P (in isoform C1)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[41] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 294) self.assertEqual(feature.location.end, 700) self.assertEqual(feature.qualifiers["note"], "Missing (in isoform C1)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[42] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 320) self.assertEqual(feature.location.end, 342) self.assertEqual( feature.qualifiers["note"], "YSAIFEENELSGWDYDYGFCSP -> LHGALPAAHCLRGLPNKRPVL (in isoform 1834, isoform 1759 and isoform EB)", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[43] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 342) self.assertEqual(feature.location.end, 700) self.assertEqual( feature.qualifiers["note"], "Missing (in isoform 1834, isoform 1759 and isoform EB)", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[44] self.assertEqual(feature.type, "VAR_SEQ") self.assertEqual(feature.location.start, 367) self.assertEqual(feature.location.end, 700) self.assertEqual( feature.qualifiers["note"], "Missing (in isoform B1 and isoform B3)" ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") feature = record.features[45] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 81) self.assertEqual(feature.location.end, 82) self.assertEqual(feature.qualifiers["note"], "I -> M (in isoform 1950)") feature = record.features[46] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 178) self.assertEqual(feature.location.end, 179) self.assertEqual(feature.qualifiers["note"], "E -> G (in isoform 1759)") feature = record.features[47] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 232) self.assertEqual(feature.location.end, 233) self.assertEqual(feature.qualifiers["note"], "I -> T (in isoform 1950)") feature = record.features[48] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 645) self.assertEqual(feature.location.end, 646) self.assertEqual(feature.qualifiers["note"], "G -> S (in isoform 1950)") feature = record.features[49] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 408) self.assertEqual(feature.location.end, 409) self.assertEqual( feature.qualifiers["note"], "D->N: Significant reduction of binding." ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:1714448") feature = record.features[50] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 435) self.assertEqual(feature.location.end, 436) self.assertEqual( feature.qualifiers["note"], "D->N: No change in binding or cAMP production." ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:1714448") feature = record.features[51] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 454) self.assertEqual(feature.location.end, 455) self.assertEqual( feature.qualifiers["note"], "E->Q: No change in binding or cAMP production." ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:1714448") feature = record.features[52] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 581) self.assertEqual(feature.location.end, 582) self.assertEqual( feature.qualifiers["note"], "D->N: No change in binding or cAMP production." ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:1714448") feature = record.features[53] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 646) self.assertEqual(feature.location.end, 647) self.assertEqual( feature.qualifiers["note"], "C->A: Trapped intracellularly and does not appear to become mature; when associated with A-648.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:7776964") feature = record.features[54] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 647) self.assertEqual(feature.location.end, 648) self.assertEqual( feature.qualifiers["note"], "C->A: Trapped intracellularly and does not appear to become mature; when associated with A-647.", ) self.assertEqual(feature.qualifiers["evidence"], "ECO:0000269|PubMed:7776964") feature = record.features[55] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 32) self.assertEqual(feature.location.end, 33) self.assertEqual(feature.qualifiers["note"], "R -> L (in Ref. 9; AA sequence)") self.assertEqual(feature.qualifiers["evidence"], "ECO:0000305") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 11) reference = record.references[0] self.assertEqual( reference.authors, "McFarland K.C., Sprengel R., Phillips H.S., Koehler M., Rosemblit N., Nikolics K., Segaloff D.L., Seeburg P.H.", ) self.assertEqual( reference.title, "Lutropin-choriogonadotropin receptor: an unusual member of the G protein-coupled receptor family.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2502842")) self.assertEqual(reference.references[1], ("DOI", "10.1126/science.2502842")) reference = record.references[1] self.assertEqual( reference.authors, "Aatsinki J.T., Pietila E.M., Lakkakorpi J.T., Rajaniemi H.J.", ) self.assertEqual( reference.title, "Expression of the LH/CG receptor gene in rat ovarian tissue is regulated by an extensive alternative splicing of the primary transcript.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1353463")) self.assertEqual( reference.references[1], ("DOI", "10.1016/0303-7207(92)90079-l") ) reference = record.references[2] self.assertEqual(reference.authors, "Koo Y.B., Slaughter R.G., Ji T.H.") self.assertEqual( reference.title, "Structure of the luteinizing hormone receptor gene and multiple exons of the coding sequence.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2019252")) self.assertEqual(reference.references[1], ("DOI", "10.1210/endo-128-5-2297")) reference = record.references[3] self.assertEqual(reference.authors, "Bernard M.P., Myers R.V., Moyle W.R.") self.assertEqual( reference.title, "Cloning of rat lutropin (LH) receptor analogs lacking the soybean lectin domain.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1976554")) self.assertEqual( reference.references[1], ("DOI", "10.1016/0303-7207(90)90034-6") ) reference = record.references[4] self.assertEqual( reference.authors, "Segaloff D.L., Sprengel R., Nikolics K., Ascoli M." ) self.assertEqual( reference.title, "Structure of the lutropin/choriogonadotropin receptor." ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2281186")) self.assertEqual( reference.references[1], ("DOI", "10.1016/b978-0-12-571146-3.50014-6") ) reference = record.references[5] self.assertEqual( reference.authors, "Tsai-Morris C.H., Buczko E., Wang W., Xie X.-Z., Dufau M.L.", ) self.assertEqual( reference.title, "Structural organization of the rat luteinizing hormone (LH) receptor gene.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2040640")) self.assertEqual( reference.references[1], ("DOI", "10.1016/s0021-9258(18)99170-2") ) reference = record.references[6] self.assertEqual( reference.authors, "Tsai-Morris C.H., Buczko E., Wang W., Dufau M.L." ) self.assertEqual( reference.title, "Intronic nature of the rat luteinizing hormone receptor gene defines a soluble receptor subspecies with hormone binding activity.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2174034")) self.assertEqual( reference.references[1], ("DOI", "10.1016/s0021-9258(17)45380-4") ) reference = record.references[7] self.assertEqual( reference.authors, "Dufau M.L., Minegishi T., Buczko E.S., Delgado C.J., Zhang R.", ) self.assertEqual( reference.title, "Characterization and structure of ovarian and testicular LH/hCG receptors.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2601325")) self.assertEqual( reference.references[1], ("DOI", "10.1016/0022-4731(89)90482-2") ) reference = record.references[8] self.assertEqual(reference.authors, "Roche P.C., Ryan R.J.") self.assertEqual( reference.title, "Purification, characterization, and amino-terminal sequence of rat ovarian receptor for luteinizing hormone/human choriogonadotropin.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "2925659")) self.assertEqual( reference.references[1], ("DOI", "10.1016/s0021-9258(18)83790-5") ) reference = record.references[9] self.assertEqual(reference.authors, "Ji I., Ji T.H.") self.assertEqual( reference.title, "Asp383 in the second transmembrane domain of the lutropin receptor is important for high affinity hormone binding and cAMP production.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "1714448")) self.assertEqual( reference.references[1], ("DOI", "10.1016/s0021-9258(18)98570-4") ) reference = record.references[10] self.assertEqual(reference.authors, "Zhu H., Wang H., Ascoli M.") self.assertEqual( reference.title, "The lutropin/choriogonadotropin receptor is palmitoylated at intracellular cysteine residues.", ) self.assertEqual(len(reference.references), 2) self.assertEqual(reference.references[0], ("PubMed", "7776964")) self.assertEqual(reference.references[1], ("DOI", "10.1210/mend.9.2.7776964")) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser records = list(SeqIO.parse(datafile, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_sp012(self): """Parsing SwissProt file sp012.""" filename = "sp012" # test the record parser datafile = os.path.join("SwissProt", filename) seq_record = SeqIO.read(datafile, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "Q9Y736") self.assertEqual(seq_record.name, "Q9Y736") self.assertEqual(seq_record.description, "UBIQUITIN.") self.assertEqual( repr(seq_record.seq), "Seq('MQIFVKTLTGKTITLEVESSDTIDNVKTKIQDKEGIPPDQQRLIFAGKQLEDGR...GGN')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "Q9Y736") self.assertEqual(record.accessions, ["Q9Y736"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Fungi", "Ascomycota", "Pezizomycotina", "Eurotiomycetes", "Onygenales", "Arthrodermataceae", "mitosporic Arthrodermataceae", "Trichophyton", ], ) self.assertEqual(record.seqinfo, (153, 17238, "01153CF30C2DEDFF")) self.assertEqual(len(record.features), 0) self.assertEqual(len(record.references), 2) self.assertEqual( record.references[0].authors, "Kano R., Nakamura Y., Watanabe S., Hasegawa A.", ) self.assertEqual( record.references[0].title, "Trichophyton mentagrophytes mRNA for ubiquitin.", ) self.assertEqual(len(record.references[0].references), 0) self.assertEqual(record.references[1].authors, "Kano R.") self.assertEqual( record.references[1].title, "Microsporum canis mRNA for ubiquitin, complete cds.", ) self.assertEqual(len(record.references[1].references), 0) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser records = list(SeqIO.parse(datafile, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_sp013(self): """Parsing SwissProt file sp013.""" filename = "sp013" # test the record parser datafile = os.path.join("SwissProt", filename) seq_record = SeqIO.read(datafile, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "P82909") self.assertEqual(seq_record.name, "P82909") self.assertEqual( seq_record.description, "MITOCHONDRIAL 28S RIBOSOMAL PROTEIN S36 (MRP-S36)." ) self.assertEqual( repr(seq_record.seq), "Seq('MGSKMASASRVVQVVKPHTPLIRFPDRRDNPKPNVSEALRSAGLPSHSSVISQH...GPE')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "P82909") self.assertEqual(record.accessions, ["P82909"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Primates", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (102, 11335, "83EF107B42E2FCFD")) self.assertEqual(len(record.features), 0) self.assertEqual(len(record.references), 2) self.assertEqual(record.references[0].authors, "Strausberg R.") self.assertEqual(record.references[0].title, "") self.assertEqual(len(record.references[0].references), 0) self.assertEqual( record.references[1].authors, "Koc E.C., Burkhart W., Blackburn K., Moseley A., Spremulli L.L.", ) self.assertEqual( record.references[1].title, "The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement ribosomal proteins present.", ) self.assertEqual(len(record.references[1].references), 0) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser records = list(SeqIO.parse(datafile, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_P60137(self): """Parsing SwissProt file P60137.txt.""" filename = "P60137.txt" # test the record parser datafile = os.path.join("SwissProt", filename) seq_record = SeqIO.read(datafile, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "P60137") self.assertEqual(seq_record.name, "PSBL_ORYSJ") self.assertEqual( seq_record.description, "RecName: Full=Photosystem II reaction center protein L {ECO:0000255|HAMAP-Rule:MF_01317}; Short=PSII-L {ECO:0000255|HAMAP-Rule:MF_01317};", ) self.assertEqual( repr(seq_record.seq), "Seq('MTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN')" ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "PSBL_ORYSJ") self.assertEqual( record.accessions, ["P60137", "O47030", "P12166", "P12167", "Q34007"] ) self.assertEqual( record.organism_classification, [ "Eukaryota", "Viridiplantae", "Streptophyta", "Embryophyta", "Tracheophyta", "Spermatophyta", "Magnoliopsida", "Liliopsida", "Poales", "Poaceae", "BOP clade", "Oryzoideae", "Oryzeae", "Oryzinae", "Oryza", "Oryza sativa", ], ) self.assertEqual(record.seqinfo, (38, 4497, "55537AEC50D25E8D")) self.assertEqual(len(record.features), 2) feature = record.features[0] self.assertEqual(feature.type, "CHAIN") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 38) self.assertEqual( feature.qualifiers["note"], "Photosystem II reaction center protein L" ) self.assertEqual(feature.id, "PRO_0000219754") feature = record.features[1] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 16) self.assertEqual(feature.location.end, 37) self.assertEqual(feature.qualifiers["note"], "Helical") self.assertEqual( feature.qualifiers["evidence"], "ECO:0000255|HAMAP-Rule:MF_01317" ) self.assertEqual(len(record.references), 2) self.assertEqual( record.references[0].authors, "Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., Mori M., Kondo C., Honji Y., Sun C.-R., Meng B.-Y., Li Y.-Q., Kanno A., Nishizawa Y., Hirai A., Shinozaki K., Sugiura M.", ) self.assertEqual( record.references[0].title, "The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals.", ) self.assertEqual(len(record.references[0].references), 2) self.assertEqual(record.references[0].references[0], ("PubMed", "2770692")) self.assertEqual( record.references[0].references[1], ("DOI", "10.1007/bf02464880") ) self.assertEqual( record.references[1].authors, "Tang J., Xia H., Cao M., Zhang X., Zeng W., Hu S., Tong W., Wang J., Wang J., Yu J., Yang H., Zhu L.", ) self.assertEqual( record.references[1].title, "A comparison of rice chloroplast genomes." ) self.assertEqual(len(record.references[1].references), 2) self.assertEqual(record.references[1].references[0], ("PubMed", "15122023")) self.assertEqual( record.references[1].references[1], ("DOI", "10.1104/pp.103.031245") ) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser records = list(SeqIO.parse(datafile, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_sp015(self): """Parsing SwissProt file sp015.""" filename = "sp015" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) self.assertEqual(seq_record.id, "IPI00383150") self.assertEqual(seq_record.name, "IPI00383150.2") self.assertEqual(seq_record.description, "") self.assertEqual( repr(seq_record.seq), "Seq('MSFQAPRRLLELAGQSLLRDQALAISVLDELPRELFPRLFVEAFTSRRCEVLKV...TPC')", ) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # test a couple of things on the record -- this is not exhaustive self.assertEqual(record.entry_name, "IPI00383150.2") self.assertEqual(record.accessions, ["IPI00383150"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Primates", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (457, 52856, "5C3151AAADBDE232")) self.assertEqual(len(record.features), 0) self.assertEqual(len(record.references), 0) # Check the two parsers agree on the essentials self.assertEqual(seq_record.seq, record.sequence) self.assertEqual(seq_record.description, record.description) self.assertEqual(seq_record.name, record.entry_name) self.assertIn(seq_record.id, record.accessions) # Now try using the iterator - note that all these # test cases have only one record. # With the SequenceParser with open(datafile) as test_handle: records = list(SeqIO.parse(test_handle, "swiss")) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SeqRecord) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].seq, seq_record.seq) self.assertEqual(records[0].description, seq_record.description) self.assertEqual(records[0].name, seq_record.name) self.assertEqual(records[0].id, seq_record.id) # With the RecordParser with open(datafile) as test_handle: records = list(SwissProt.parse(test_handle)) self.assertEqual(len(records), 1) self.assertIsInstance(records[0], SwissProt.Record) # Check matches what we got earlier without the iterator: self.assertEqual(records[0].sequence, record.sequence) self.assertEqual(records[0].description, record.description) self.assertEqual(records[0].entry_name, record.entry_name) self.assertEqual(records[0].accessions, record.accessions) def test_P0CK95(self): """Parsing SwissProt file P0CK95.txt.""" filename = "P0CK95.txt" datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: record = SwissProt.read(test_handle) # Check the simple variant self.assertEqual( record.features[5].qualifiers["note"], "N -> G (in strain: O15:H- / 83/39 /ETEC)", ) # Check a FT where the 2nd line starts with / self.assertEqual( record.features[6].qualifiers["note"], "DGTPLPEFYSE -> EGELPKFFSD (in strain: O15:H- / 83/39 / ETEC)", ) def test_Q7Z739(self): """Parsing SwissProt file Q7Z739.txt, which has new qualifiers for ligands from Uniprot version 2022_03.""" filename = "Q7Z739.txt" datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: record = SwissProt.read(test_handle) self.assertEqual( record.gene_name, [ { "Name": "YTHDF3 {ECO:0000303|PubMed:28106072, ECO:0000312|HGNC:HGNC:26465}" } ], ) # Check the new ligand feature self.assertEqual(record.features[10].qualifiers["ligand"], "RNA") self.assertEqual( record.features[10].qualifiers["ligand_id"], "ChEBI:CHEBI:33697" ) self.assertEqual( record.features[10].qualifiers["ligand_part"], "N(6)-methyladenosine 5'-phosphate residue", ) self.assertEqual( record.features[10].qualifiers["ligand_part_id"], "ChEBI:CHEBI:74449" ) def test_ft_line(self): """Parsing SwissProt file O23729, which has a new-style FT line.""" filename = "O23729.txt" datafile = os.path.join("SwissProt", filename) with open(datafile) as test_handle: record = SwissProt.read(test_handle) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)