# 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_sp001(self): """Parsing SwissProt file sp001.""" filename = "sp001" # 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, "N33_HUMAN") self.assertEqual(seq_record.description, "N33 PROTEIN.") 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, "N33_HUMAN") self.assertEqual(record.accessions, ["Q13454", "Q14911", "Q14912"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Mammalia", "Eutheria", "Primates", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (348, 39676, "75818910")) self.assertEqual(len(record.features), 6) feature = record.features[0] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 19) self.assertEqual(feature.location.end, 40) self.assertEqual(feature.qualifiers["description"], "POTENTIAL.") self.assertIsNone(feature.id) feature = record.features[1] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 196) self.assertEqual(feature.location.end, 217) self.assertEqual(feature.qualifiers["description"], "POTENTIAL.") self.assertIsNone(feature.id) feature = record.features[2] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 221) self.assertEqual(feature.location.end, 242) self.assertEqual(feature.qualifiers["description"], "POTENTIAL.") self.assertIsNone(feature.id) feature = record.features[3] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 276) self.assertEqual(feature.location.end, 297) self.assertEqual(feature.qualifiers["description"], "POTENTIAL.") self.assertIsNone(feature.id) feature = record.features[4] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 312) self.assertEqual(feature.location.end, 333) self.assertEqual(feature.qualifiers["description"], "POTENTIAL.") self.assertIsNone(feature.id) feature = record.features[5] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 343) self.assertEqual(feature.location.end, 348) self.assertEqual( feature.qualifiers["description"], "DLDFE -> FLIK (IN FORM 2)." ) self.assertIsNone(feature.id) self.assertEqual(len(record.references), 1) 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(len(record.references[0].references), 1) self.assertEqual(record.references[0].references[0], ("MEDLINE", "96299740")) # Check that the two parsers agree on the essentials self.assertEqual(str(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(str(records[0].seq), str(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_sp002(self): """Parsing SwissProt file sp002.""" filename = "sp002" # 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, "P54101") self.assertEqual(seq_record.name, "CSP_MOUSE") self.assertEqual(seq_record.description, "CYSTEINE STRING PROTEIN (CSP).") 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, "CSP_MOUSE") self.assertEqual(record.accessions, ["P54101"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Mammalia", "Eutheria", "Rodentia", "Sciurognathi", "Muridae", "Murinae", "Mus", ], ) self.assertEqual(record.seqinfo, (198, 22100, "9DF0142B")) self.assertEqual(len(record.features), 2) feature = record.features[0] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 12) self.assertEqual(feature.location.end, 82) self.assertEqual(feature.qualifiers["description"], "DNAJ-LIKE.") self.assertIsNone(feature.id) feature = record.features[1] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 117) self.assertEqual(feature.location.end, 128) self.assertEqual(feature.qualifiers["description"], "POLY-CYS.") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 3) self.assertEqual(record.references[0].authors, "QIN N., LIN T., BIRNBAUMER L.") self.assertEqual(record.references[0].title, "") self.assertEqual(len(record.references[0].references), 0) self.assertEqual( record.references[1].authors, "MASTROGIACOMO A., GUNDERSEN C.B." ) self.assertEqual( record.references[1].title, "The nucleotide and deduced amino acid sequence of a rat cysteine string protein.", ) self.assertEqual(len(record.references[1].references), 1) self.assertEqual(record.references[1].references[0], ("MEDLINE", "95223109")) self.assertEqual(record.references[2].authors, "BRAUN J.E., SCHELLER R.H.") self.assertEqual( record.references[2].title, "Cysteine string protein, a DnaJ family member, is present on diverse secretory vesicles.", ) self.assertEqual(len(record.references[2].references), 1) self.assertEqual(record.references[2].references[0], ("MEDLINE", "96188189")) # Check the two parsers agree on the essentials self.assertEqual(str(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(str(records[0].seq), str(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_sp003(self): """Parsing SwissProt file sp003.""" filename = "sp003" # 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, "P42655") self.assertEqual(seq_record.name, "143E_HUMAN") self.assertEqual( seq_record.description, "14-3-3 PROTEIN EPSILON (MITOCHONDRIAL IMPORT STIMULATION FACTOR L SUBUNIT) (PROTEIN KINASE C INHIBITOR PROTEIN-1) (KCIP-1) (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, "143E_HUMAN") self.assertEqual(record.accessions, ["P42655", "P29360", "Q63631"]) self.assertEqual( record.organism_classification, [ "EUKARYOTA", "METAZOA", "CHORDATA", "VERTEBRATA", "MAMMALIA", "EUTHERIA", "PRIMATES", "CATARRHINI", "HOMINIDAE", "HOMO", ], ) self.assertEqual(record.seqinfo, (255, 29174, "40A43E62")) self.assertEqual(len(record.features), 5) feature = record.features[0] self.assertEqual(feature.type, "MOD_RES") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 1) self.assertEqual(feature.qualifiers["description"], "ACETYLATION.") self.assertIsNone(feature.id) feature = record.features[1] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 72) self.assertEqual(feature.location.end, 73) self.assertEqual(feature.qualifiers["description"], "K -> T (IN REF. 8).") self.assertIsNone(feature.id) feature = record.features[2] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 119) self.assertEqual(feature.location.end, 120) self.assertEqual(feature.qualifiers["description"], "F -> S (IN REF. 8).") self.assertIsNone(feature.id) feature = record.features[3] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 122) self.assertEqual(feature.location.end, 123) self.assertEqual(feature.qualifiers["description"], "K -> Y (IN REF. 8).") self.assertIsNone(feature.id) feature = record.features[4] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 128) self.assertEqual(feature.location.end, 129) self.assertEqual(feature.qualifiers["description"], "H -> Y (IN REF. 13).") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 13) self.assertEqual( record.references[0].authors, "CONKLIN D.S., GALAKTIONOV K., BEACH D." ) self.assertEqual( record.references[0].title, "14-3-3 proteins associate with cdc25 phosphatases.", ) self.assertEqual(len(record.references[0].references), 1) self.assertEqual(record.references[0].references[0], ("MEDLINE", "95372385")) self.assertEqual( record.references[1].authors, "LUK S.C.W., LEE C.Y., WAYE M.M.Y." ) self.assertEqual(record.references[1].title, "") self.assertEqual(len(record.references[1].references), 0) self.assertEqual( record.references[2].authors, "JIN D.Y., LYU M.S., KOZAK C.A., JEANG K.T." ) self.assertEqual(record.references[2].title, "Function of 14-3-3 proteins.") self.assertEqual(len(record.references[2].references), 1) self.assertEqual(record.references[2].references[0], ("MEDLINE", "96300316")) self.assertEqual( record.references[3].authors, "CHONG S.S., TANIGAMI A., ROSCHKE A.V., LEDBETTER D.H.", ) self.assertEqual( record.references[3].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(record.references[3].references), 1) self.assertEqual(record.references[3].references[0], ("MEDLINE", "97011338")) self.assertEqual( record.references[4].authors, "TANIGAMI A., CHONG S.S., LEDBETTER D.H." ) self.assertEqual(record.references[4].title, "14-3-3 epsilon genomic sequence.") self.assertEqual(len(record.references[4].references), 0) self.assertEqual( record.references[5].authors, "ROSEBOOM P.H., WELLER J.L., BABILA T., AITKEN A., SELLERS L.A., MOFFET J.R., NAMBOODIRI M.A., KLEIN D.C.", ) self.assertEqual( record.references[5].title, "Cloning and characterization of the epsilon and zeta isoforms of the 14-3-3 proteins.", ) self.assertEqual(len(record.references[5].references), 1) self.assertEqual(record.references[5].references[0], ("MEDLINE", "94296566")) self.assertEqual( record.references[6].authors, "ALAM R., HACHIYA N., SAKAGUCHI M., SHUN-ICHIRO K., IWANAGA S., KITAJIMA M., MIHARA K., OMURA T.", ) self.assertEqual( record.references[6].title, "cDNA cloning and characterization of mitochondrial import stimulation factor (MSF) purified from rat liver cytosol.", ) self.assertEqual(len(record.references[6].references), 1) self.assertEqual(record.references[6].references[0], ("MEDLINE", "95122474")) self.assertEqual( record.references[7].authors, "GAO L., GU X.B., YU D.S., YU R.K., ZENG G." ) self.assertEqual( record.references[7].title, "Association of a 14-3-3 protein with CMP-NeuAc:GM1 alpha 2,3-sialyltransferase.", ) self.assertEqual(len(record.references[7].references), 1) self.assertEqual(record.references[7].references[0], ("MEDLINE", "96280718")) self.assertEqual( record.references[8].authors, "MCCONNELL J.E., ARMSTRONG J.F., BARD J.B." ) self.assertEqual( record.references[8].title, "The mouse 14-3-3 epsilon isoform, a kinase regulator whose expression pattern is modulated in mesenchyme and neuronal differentiation.", ) self.assertEqual(len(record.references[8].references), 1) self.assertEqual(record.references[8].references[0], ("MEDLINE", "95269876")) self.assertEqual( record.references[9].authors, "TAKIHARA Y., IRIE K., NOMURA M., MOTALEB M., MATSUMOTO K., SHIMADA K.", ) self.assertEqual(record.references[9].title, "") self.assertEqual(len(record.references[9].references), 0) self.assertEqual( record.references[10].authors, "JONES J.M., NIIKURA T., PINKE R.M., GUO W., MOLDAY L., LEYKAM J., MCCONNELL D.G.", ) self.assertEqual( record.references[10].title, "Expression of 14-3-3 proteins in bovine retinal photoreceptors.", ) self.assertEqual(len(record.references[10].references), 0) self.assertEqual( record.references[11].authors, "TOKER A., SELLERS L.A., AMESS B., PATEL Y., HARRIS A., AITKEN A.", ) self.assertEqual( record.references[11].title, "Multiple isoforms of a protein kinase C inhibitor (KCIP-1/14-3-3) from sheep brain. Amino acid sequence of phosphorylated forms.", ) self.assertEqual(len(record.references[11].references), 1) self.assertEqual(record.references[11].references[0], ("MEDLINE", "92283271")) self.assertEqual( record.references[12].authors, "TOKER A., ELLIS C.A., SELLERS L.A., AITKEN A.", ) self.assertEqual( record.references[12].title, "Protein kinase C inhibitor proteins. Purification from sheep brain and sequence similarity to lipocortins and 14-3-3 protein.", ) self.assertEqual(len(record.references[12].references), 1) self.assertEqual(record.references[12].references[0], ("MEDLINE", "90345949")) # Check the two parsers agree on the essentials self.assertEqual(str(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(str(records[0].seq), str(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(str(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(str(records[0].seq), str(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_sp005(self): """Parsing SwissProt file sp005.""" filename = "sp005" # 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, "P24973") self.assertEqual(seq_record.name, "NU3M_BALPH") self.assertEqual( seq_record.description, "NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 3 (EC 1.6.5.3).", ) 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, ["P24973"]) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Mammalia", "Eutheria", "Cetartiodactyla", "Cetacea", "Mysticeti", "Balaenopteridae", "Balaenoptera", ], ) self.assertEqual(record.seqinfo, (115, 13022, "ACF02965")) self.assertEqual(len(record.features), 0) self.assertEqual(len(record.references), 2) self.assertEqual( record.references[0].authors, "ARNASON U., GULLBERG A., WIDEGREN B." ) self.assertEqual( record.references[0].title, "The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus.", ) self.assertEqual(len(record.references[0].references), 1) self.assertEqual(record.references[0].references[0], ("MEDLINE", "92139449")) self.assertEqual(record.references[1].authors, "ARNASON U., GULLBERG A.") self.assertEqual( record.references[1].title, "Comparison between the complete mtDNA sequences of the blue and the fin whale, two species that can hybridize in nature.", ) self.assertEqual(len(record.references[1].references), 1) self.assertEqual(record.references[1].references[0], ("MEDLINE", "94141932")) # Check the two parsers agree on the essentials self.assertEqual(str(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(str(records[0].seq), str(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_sp006(self): """Parsing SwissProt file sp006.""" filename = "sp006" # 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, "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", "FIRMICUTES", "ACTINOBACTERIA", "ACTINOBACTERIDAE", "ACTINOMYCETALES", "STREPTOMYCINEAE", "STREPTOMYCETACEAE", "STREPTOMYCES", ], ) self.assertEqual(record.seqinfo, (339, 37035, "848B7337")) self.assertEqual(len(record.features), 0) self.assertEqual(len(record.references), 1) self.assertEqual( record.references[0].authors, "SUMMERS R.G., WENDT-PIENKOWSKI E., MOTAMEDI H., HUTCHINSON C.R.", ) self.assertEqual( record.references[0].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(record.references[0].references), 1) self.assertEqual(record.references[0].references[0], ("MEDLINE", "92193265")) # Check the two parsers agree on the essentials self.assertEqual(str(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(str(records[0].seq), str(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_sp007(self): """Parsing SwissProt file sp007.""" filename = "sp007" # 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, "CLAUDIN-1 (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", "Mammalia", "Eutheria", "Primates", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (211, 22744, "07269000E6C214F0")) self.assertEqual(len(record.features), 6) feature = record.features[0] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 7) self.assertEqual(feature.location.end, 28) self.assertEqual(feature.qualifiers["description"], "POTENTIAL.") self.assertIsNone(feature.id) feature = record.features[1] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 81) self.assertEqual(feature.location.end, 102) self.assertEqual(feature.qualifiers["description"], "POTENTIAL.") self.assertIsNone(feature.id) feature = record.features[2] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 115) self.assertEqual(feature.location.end, 136) self.assertEqual(feature.qualifiers["description"], "POTENTIAL.") self.assertIsNone(feature.id) feature = record.features[3] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 163) self.assertEqual(feature.location.end, 184) self.assertEqual(feature.qualifiers["description"], "POTENTIAL.") self.assertIsNone(feature.id) feature = record.features[4] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 61) self.assertEqual(feature.location.end, 62) self.assertEqual(feature.qualifiers["description"], "I -> V (IN REF. 2).") self.assertIsNone(feature.id) feature = record.features[5] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 134) self.assertEqual(feature.location.end, 135) self.assertEqual(feature.qualifiers["description"], "V -> A (IN REF. 2).") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 2) self.assertEqual( record.references[0].authors, "Swisshelm K.L., Machl A., Planitzer S., Robertson R., Kubbies M., Hosier S.", ) self.assertEqual( record.references[0].title, "SEMP1, a senescence-associated cDNA isolated from human mammary epithelial cells, is a member of an epithelial membrane protein superfamily.", ) self.assertEqual(len(record.references[0].references), 1) self.assertEqual(record.references[0].references[0], ("MEDLINE", "99132301")) self.assertEqual(record.references[1].authors, "Mitic L.M., Anderson J.M.") self.assertEqual( record.references[1].title, "Human claudin-1 isolated from Caco-2 mRNA." ) self.assertEqual(len(record.references[1].references), 0) # Check the two parsers agree on the essentials self.assertEqual(str(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(str(records[0].seq), str(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_sp008(self): """Parsing SwissProt file sp008.""" filename = "sp008" # 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, "P01892") self.assertEqual(seq_record.name, "1A02_HUMAN") self.assertEqual( seq_record.description, "HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN PRECURSOR.", ) self.assertEqual( repr(seq_record.seq), "Seq('MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDD...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, "1A02_HUMAN") self.assertEqual( record.accessions, [ "P01892", "P06338", "P30514", "P30444", "P30445", "P30446", "Q29680", "Q29899", "Q95352", "Q29837", "Q95380", ], ) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Mammalia", "Eutheria", "Primates", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (365, 40922, "B54A97B24B337C08")) self.assertEqual(len(record.features), 71) 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["description"], "") self.assertIsNone(feature.id) 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["description"], "HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN.", ) self.assertIsNone(feature.id) feature = record.features[2] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 24) self.assertEqual(feature.location.end, 114) self.assertEqual(feature.qualifiers["description"], "EXTRACELLULAR ALPHA-1.") self.assertIsNone(feature.id) feature = record.features[3] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 114) self.assertEqual(feature.location.end, 206) self.assertEqual(feature.qualifiers["description"], "EXTRACELLULAR ALPHA-2.") self.assertIsNone(feature.id) feature = record.features[4] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 206) self.assertEqual(feature.location.end, 298) self.assertEqual(feature.qualifiers["description"], "EXTRACELLULAR ALPHA-3.") self.assertIsNone(feature.id) feature = record.features[5] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 298) self.assertEqual(feature.location.end, 308) self.assertEqual(feature.qualifiers["description"], "CONNECTING PEPTIDE.") self.assertIsNone(feature.id) feature = record.features[6] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 308) self.assertEqual(feature.location.end, 332) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[7] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 332) self.assertEqual(feature.location.end, 365) self.assertEqual(feature.qualifiers["description"], "CYTOPLASMIC TAIL.") self.assertIsNone(feature.id) feature = record.features[8] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 109) self.assertEqual(feature.location.end, 110) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[9] self.assertEqual(feature.type, "DISULFID") self.assertEqual(feature.location.start, 124) self.assertEqual(feature.location.end, 188) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[10] self.assertEqual(feature.type, "DISULFID") self.assertEqual(feature.location.start, 226) self.assertEqual(feature.location.end, 283) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[11] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 26) self.assertEqual(feature.location.end, 36) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[12] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 44) self.assertEqual(feature.location.end, 52) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[13] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 52) self.assertEqual(feature.location.end, 54) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[14] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 54) self.assertEqual(feature.location.end, 61) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[15] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 61) self.assertEqual(feature.location.end, 63) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[16] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 69) self.assertEqual(feature.location.end, 71) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[17] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 73) self.assertEqual(feature.location.end, 76) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[18] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 76) self.assertEqual(feature.location.end, 78) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[19] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 80) self.assertEqual(feature.location.end, 108) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[20] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 108) self.assertEqual(feature.location.end, 110) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[21] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 112) self.assertEqual(feature.location.end, 114) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[22] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 117) self.assertEqual(feature.location.end, 127) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[23] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 128) self.assertEqual(feature.location.end, 130) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[24] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 132) self.assertEqual(feature.location.end, 142) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[25] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 142) self.assertEqual(feature.location.end, 144) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[26] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 144) self.assertEqual(feature.location.end, 150) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[27] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 151) self.assertEqual(feature.location.end, 153) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[28] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 156) self.assertEqual(feature.location.end, 159) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[29] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 162) self.assertEqual(feature.location.end, 163) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[30] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 163) self.assertEqual(feature.location.end, 173) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[31] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 173) self.assertEqual(feature.location.end, 175) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[32] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 185) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[33] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 185) self.assertEqual(feature.location.end, 186) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[34] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 186) self.assertEqual(feature.location.end, 198) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[35] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 198) self.assertEqual(feature.location.end, 199) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[36] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 199) self.assertEqual(feature.location.end, 203) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[37] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 203) self.assertEqual(feature.location.end, 204) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[38] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 206) self.assertEqual(feature.location.end, 207) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[39] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 209) self.assertEqual(feature.location.end, 219) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[40] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 219) self.assertEqual(feature.location.end, 221) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[41] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 221) self.assertEqual(feature.location.end, 233) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[42] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 237) self.assertEqual(feature.location.end, 243) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[43] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 243) self.assertEqual(feature.location.end, 245) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[44] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 245) self.assertEqual(feature.location.end, 247) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[45] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 248) self.assertEqual(feature.location.end, 251) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[46] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 252) self.assertEqual(feature.location.end, 254) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[47] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 257) self.assertEqual(feature.location.end, 259) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[48] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 264) self.assertEqual(feature.location.end, 274) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[49] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 274) self.assertEqual(feature.location.end, 276) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[50] self.assertEqual(feature.type, "HELIX") self.assertEqual(feature.location.start, 277) self.assertEqual(feature.location.end, 280) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[51] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 280) self.assertEqual(feature.location.end, 286) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[52] self.assertEqual(feature.type, "TURN") self.assertEqual(feature.location.start, 287) self.assertEqual(feature.location.end, 289) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[53] self.assertEqual(feature.type, "STRAND") self.assertEqual(feature.location.start, 293) self.assertEqual(feature.location.end, 297) self.assertEqual(feature.qualifiers["description"], "") self.assertIsNone(feature.id) feature = record.features[54] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 32) self.assertEqual(feature.location.end, 33) self.assertEqual( feature.qualifiers["description"], "F -> Y (IN A*0205, A*0206, A*0208, A*0210 AND A*0221).", ) self.assertEqual(feature.id, "VAR_004334") feature = record.features[55] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 53) self.assertEqual(feature.location.end, 54) self.assertEqual(feature.qualifiers["description"], "D -> N (IN A*0221).") self.assertEqual(feature.id, "VAR_004335") feature = record.features[56] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 66) self.assertEqual(feature.location.end, 67) self.assertEqual( feature.qualifiers["description"], "Q -> R (IN A*0202, A*0205, AND A*0208)." ) self.assertEqual(feature.id, "VAR_004336") feature = record.features[57] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 89) self.assertEqual(feature.location.end, 90) self.assertEqual( feature.qualifiers["description"], "K -> N (IN A*0208 AND A*0220)." ) self.assertEqual(feature.id, "VAR_004337") feature = record.features[58] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 96) self.assertEqual(feature.location.end, 98) self.assertEqual(feature.qualifiers["description"], "TH -> ID (IN A*0211).") self.assertEqual(feature.id, "VAR_004338") feature = record.features[59] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 118) self.assertEqual(feature.location.end, 119) self.assertEqual( feature.qualifiers["description"], "V -> L (IN A*0202, A*0205, A*0208 AND A*0217).", ) self.assertEqual(feature.id, "VAR_004339") feature = record.features[60] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 120) self.assertEqual(feature.location.end, 121) self.assertEqual( feature.qualifiers["description"], "R -> M (IN A*0204 AND A*0217)." ) self.assertEqual(feature.id, "VAR_004340") feature = record.features[61] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 122) self.assertEqual(feature.location.end, 123) self.assertEqual( feature.qualifiers["description"], "Y -> C (IN A*0207 AND A*0218)." ) self.assertEqual(feature.id, "VAR_004341") feature = record.features[62] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 122) self.assertEqual(feature.location.end, 123) self.assertEqual( feature.qualifiers["description"], "Y -> F (IN A*0210 AND A*0217)." ) self.assertEqual(feature.id, "VAR_004342") feature = record.features[63] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 130) self.assertEqual(feature.location.end, 131) self.assertEqual(feature.qualifiers["description"], "W -> G (IN A*0210).") self.assertEqual(feature.id, "VAR_004343") feature = record.features[64] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 161) self.assertEqual(feature.location.end, 162) self.assertEqual(feature.qualifiers["description"], "M -> K (IN A*0218).") self.assertEqual(feature.id, "VAR_004344") feature = record.features[65] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 172) self.assertEqual(feature.location.end, 173) self.assertEqual(feature.qualifiers["description"], "A -> T (IN A*0203).") self.assertEqual(feature.id, "VAR_004345") feature = record.features[66] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 176) self.assertEqual( feature.qualifiers["description"], "V -> E (IN A*0203 AND A*0213)." ) self.assertEqual(feature.id, "VAR_004346") feature = record.features[67] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 179) self.assertEqual(feature.location.end, 180) self.assertEqual( feature.qualifiers["description"], "L -> W (IN A*0202, A*0203, A*0205 AND A*0208).", ) self.assertEqual(feature.id, "VAR_004347") feature = record.features[68] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 179) self.assertEqual(feature.location.end, 180) self.assertEqual( feature.qualifiers["description"], "L -> Q (IN A*0212 AND A*0213)." ) self.assertEqual(feature.id, "VAR_004348") feature = record.features[69] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 186) self.assertEqual(feature.location.end, 187) self.assertEqual(feature.qualifiers["description"], "T -> E (IN A*0216).") self.assertEqual(feature.id, "VAR_004349") feature = record.features[70] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 259) self.assertEqual(feature.location.end, 260) self.assertEqual(feature.qualifiers["description"], "A -> E (IN A*0209).") self.assertEqual(feature.id, "VAR_004350") self.assertEqual(len(record.references), 27) self.assertEqual(record.references[0].authors, "Koller B.H., Orr H.T.") self.assertEqual( record.references[0].title, "Cloning and complete sequence of an HLA-A2 gene: analysis of two HLA-A alleles at the nucleotide level.", ) self.assertEqual(len(record.references[0].references), 1) self.assertEqual(record.references[0].references[0], ("MEDLINE", "85132727")) self.assertEqual( record.references[1].authors, "Cianetti L., Testa U., Scotto L., la Valle R., Simeone A., Boccoli G., Giannella G., Peschle C., Boncinelli E.", ) self.assertEqual( record.references[1].title, "Three new class I HLA alleles: structure of mRNAs and alternative mechanisms of processing.", ) self.assertEqual(len(record.references[1].references), 1) self.assertEqual(record.references[1].references[0], ("MEDLINE", "89122144")) self.assertEqual( record.references[2].authors, "Ennis P.D., Zemmour J., Salter R.D., Parham P.", ) self.assertEqual( record.references[2].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(record.references[2].references), 1) self.assertEqual(record.references[2].references[0], ("MEDLINE", "90207291")) self.assertEqual( record.references[3].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( record.references[3].title, "Unusual HLA-B alleles in two tribes of Brazilian Indians.", ) self.assertEqual(len(record.references[3].references), 1) self.assertEqual(record.references[3].references[0], ("MEDLINE", "92269955")) self.assertEqual(record.references[4].authors, "Krangel M.S.") self.assertEqual( record.references[4].title, "Unusual RNA splicing generates a secreted form of HLA-A2 in a mutagenized B lymphoblastoid cell line.", ) self.assertEqual(len(record.references[4].references), 1) self.assertEqual(record.references[4].references[0], ("MEDLINE", "85230571")) self.assertEqual( record.references[5].authors, "Orr H.T., Lopez de Castro J.A., Parham P., Ploegh H.L., Strominger J.L.", ) self.assertEqual( record.references[5].title, "Comparison of amino acid sequences of two human histocompatibility antigens, HLA-A2 and HLA-B7: location of putative alloantigenic sites.", ) self.assertEqual(len(record.references[5].references), 1) self.assertEqual(record.references[5].references[0], ("MEDLINE", "80056745")) self.assertEqual( record.references[6].authors, "Lopez de Castro J.A., Strominger J.L., Strong D.M., Orr H.T.", ) self.assertEqual( record.references[6].title, "Structure of crossreactive human histocompatibility antigens HLA-A28 and HLA-A2: possible implications for the generation of HLA polymorphism.", ) self.assertEqual(len(record.references[6].references), 1) self.assertEqual(record.references[6].references[0], ("MEDLINE", "82247941")) self.assertEqual( record.references[7].authors, "Mattson D.H., Handy D.E., Bradley D.A., Coligan J.E., Cowan E.P., Biddison W.E.", ) self.assertEqual( record.references[7].title, "DNA sequences of the genes that encode the CTL-defined HLA-A2 variants M7 and DK1.", ) self.assertEqual(len(record.references[7].references), 1) self.assertEqual(record.references[7].references[0], ("MEDLINE", "87306734")) self.assertEqual( record.references[8].authors, "Holmes N., Ennis P., Wan A.M., Denney D.W., Parham P.", ) self.assertEqual( record.references[8].title, "Multiple genetic mechanisms have contributed to the generation of the HLA-A2/A28 family of class I MHC molecules.", ) self.assertEqual(len(record.references[8].references), 1) self.assertEqual(record.references[8].references[0], ("MEDLINE", "87252273")) self.assertEqual(record.references[9].authors, "Domena J.D.") self.assertEqual(record.references[9].title, "") self.assertEqual(len(record.references[9].references), 0) self.assertEqual( record.references[10].authors, "Castano A.R., Lopez de Castro J.A." ) self.assertEqual( record.references[10].title, "Structure of the HLA-A*0204 antigen, found in South American Indians. Spatial clustering of HLA-A2 subtype polymorphism.", ) self.assertEqual(len(record.references[10].references), 1) self.assertEqual(record.references[10].references[0], ("MEDLINE", "92039809")) self.assertEqual( record.references[11].authors, "Watkins D.I., McAdam S.N., Liu X., Stang C.R., Milford E.L., Levine C.G., Garber T.L., Dogon A.L., Lord C.I., Ghim S.H., Troup G.M., Hughes A.L., Letvin N.L.", ) self.assertEqual( record.references[11].title, "New recombinant HLA-B alleles in a tribe of South American Amerindians indicate rapid evolution of MHC class I loci.", ) self.assertEqual(len(record.references[11].references), 1) self.assertEqual(record.references[11].references[0], ("MEDLINE", "92269956")) self.assertEqual( record.references[12].authors, "Parham P., Lawlor D.A., Lomen C.E., Ennis P.D.", ) self.assertEqual( record.references[12].title, "Diversity and diversification of HLA-A,B,C alleles.", ) self.assertEqual(len(record.references[12].references), 1) self.assertEqual(record.references[12].references[0], ("MEDLINE", "89235215")) self.assertEqual( record.references[13].authors, "Ezquerra A., Domenech N., van der Poel J., Strominger J.L., Vega M.A., Lopez de Castro J.A.", ) self.assertEqual( record.references[13].title, "Molecular analysis of an HLA-A2 functional variant CLA defined by cytolytic T lymphocytes.", ) self.assertEqual(len(record.references[13].references), 1) self.assertEqual(record.references[13].references[0], ("MEDLINE", "86305811")) self.assertEqual( record.references[14].authors, "Domenech N., Ezquerra A., Castano R., Lopez de Castro J.A.", ) self.assertEqual( record.references[14].title, "Structural analysis of HLA-A2.4 functional variant KNE. Implications for the mapping of HLA-A2-specific T-cell epitopes.", ) self.assertEqual(len(record.references[14].references), 1) self.assertEqual(record.references[14].references[0], ("MEDLINE", "88113844")) self.assertEqual( record.references[15].authors, "Domenech N., Castano R., Goulmy E., Lopez de Castro J.A.", ) self.assertEqual( record.references[15].title, "Molecular analysis of HLA-A2.4 functional variant KLO: close structural and evolutionary relatedness to the HLA-A2.2 subtype.", ) self.assertEqual(len(record.references[15].references), 1) self.assertEqual(record.references[15].references[0], ("MEDLINE", "88314183")) self.assertEqual( record.references[16].authors, "Castano R., Ezquerra A., Domenech N., Lopez de Castro J.A.", ) self.assertEqual( record.references[16].title, "An HLA-A2 population variant with structural polymorphism in the alpha 3 region.", ) self.assertEqual(len(record.references[16].references), 1) self.assertEqual(record.references[16].references[0], ("MEDLINE", "88186100")) self.assertEqual( record.references[17].authors, "Epstein H., Kennedy L., Holmes N." ) self.assertEqual( record.references[17].title, "An Oriental HLA-A2 subtype is closely related to a subset of Caucasoid HLA-A2 alleles.", ) self.assertEqual(len(record.references[17].references), 1) self.assertEqual(record.references[17].references[0], ("MEDLINE", "89122133")) self.assertEqual( record.references[18].authors, "Castano A.R., Lopez de Castro J.A." ) self.assertEqual( record.references[18].title, "Structure of the HLA-A*0211 (A2.5) subtype: further evidence for selection-driven diversification of HLA-A2 antigens.", ) self.assertEqual(len(record.references[18].references), 1) self.assertEqual(record.references[18].references[0], ("MEDLINE", "92218010")) self.assertEqual( record.references[19].authors, "Barber D.F., Fernandez J.M., Lopez de Castro J.A.", ) self.assertEqual( record.references[19].title, "Primary structure of a new HLA-A2 subtype: HLA-A*0213.", ) self.assertEqual(len(record.references[19].references), 1) self.assertEqual(record.references[19].references[0], ("MEDLINE", "94222455")) self.assertEqual( record.references[20].authors, "Barouch D., Krausa P., Bodmer J., Browning M.J., McMichael A.J.", ) self.assertEqual( record.references[20].title, "Identification of a novel HLA-A2 subtype, HLA-A*0216.", ) self.assertEqual(len(record.references[20].references), 1) self.assertEqual(record.references[20].references[0], ("MEDLINE", "95278976")) self.assertEqual( record.references[21].authors, "Selvakumar A., Granja C.B., Salazar M., Alosco S.M., Yunis E.J., Dupont B.", ) self.assertEqual( record.references[21].title, "A novel subtype of A2 (A*0217) isolated from the South American Indian B-cell line AMALA.", ) self.assertEqual(len(record.references[21].references), 1) self.assertEqual(record.references[21].references[0], ("MEDLINE", "95381236")) self.assertEqual( record.references[22].authors, "Kashiwase K., Tokunaga K., Ishikawa Y., Oohashi H., Hashimoto M., Akaza T., Tadokoro K., Juji T.", ) self.assertEqual( record.references[22].title, "A new A2 sequence HLA-A2K from Japanese." ) self.assertEqual(len(record.references[22].references), 0) self.assertEqual( record.references[23].authors, "Fleischhauer K., Zino E., Mazzi B., Severini G.M., Benazzi E., Bordignon C.", ) self.assertEqual( record.references[23].title, "HLA-A*02 subtype distribution in Caucasians from northern Italy: identification of A*0220.", ) self.assertEqual(len(record.references[23].references), 1) self.assertEqual(record.references[23].references[0], ("MEDLINE", "97161038")) self.assertEqual(record.references[24].authors, "Szmania S., Baxter-Lowe L.A.") self.assertEqual( record.references[24].title, "Nucleotide sequence of a novel HLA-A2 gene." ) self.assertEqual(len(record.references[24].references), 0) self.assertEqual( record.references[25].authors, "Bjorkman P.J., Saper M.A., Samraoui B., Bennett W.S., Strominger J.L., Wiley D.C.", ) self.assertEqual( record.references[25].title, "Structure of the human class I histocompatibility antigen, HLA-A2.", ) self.assertEqual(len(record.references[25].references), 1) self.assertEqual(record.references[25].references[0], ("MEDLINE", "88014204")) self.assertEqual( record.references[26].authors, "Saper M.A., Bjorkman P.J., Wiley D.C." ) self.assertEqual( record.references[26].title, "Refined structure of the human histocompatibility antigen HLA-A2 at 2.6-A resolution.", ) self.assertEqual(len(record.references[26].references), 1) self.assertEqual(record.references[26].references[0], ("MEDLINE", "91245570")) # Check the two parsers agree on the essentials self.assertEqual(str(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(str(records[0].seq), str(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_sp009(self): """Parsing SwissProt file sp009.""" filename = "sp009" # 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, "CHALCONE SYNTHASE 3 (EC 2.3.1.74) (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", "Embryophyta", "Tracheophyta", "Spermatophyta", "Magnoliophyta", "Liliopsida", "Asparagales", "Orchidaceae", "Bromheadia", ], ) self.assertEqual(record.seqinfo, (394, 42941, "2F8D14AF4870BBB2")) self.assertEqual(len(record.features), 1) feature = record.features[0] self.assertEqual(feature.type, "ACT_SITE") self.assertEqual(feature.location.start, 164) self.assertEqual(feature.location.end, 165) self.assertEqual(feature.qualifiers["description"], "BY SIMILARITY.") 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(str(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(str(records[0].seq), str(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_sp010(self): """Parsing SwissProt file sp010.""" filename = "sp010" # 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, "Q13639") self.assertEqual(seq_record.name, "5H4_HUMAN") self.assertEqual( seq_record.description, "5-HYDROXYTRYPTAMINE 4 RECEPTOR (5-HT-4) (SEROTONIN RECEPTOR) (5-HT4).", ) 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, "5H4_HUMAN") self.assertEqual( record.accessions, ["Q13639", "Q9UBM6", "Q9UQR6", "Q9UE22", "Q9UE23", "Q9UBT4", "Q9NY73"], ) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Primates", "Catarrhini", "Hominidae", "Homo", ], ) self.assertEqual(record.seqinfo, (388, 43761, "7FCFEC60E7BDF560")) self.assertEqual(len(record.features), 23) feature = record.features[0] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 0) self.assertEqual(feature.location.end, 19) self.assertEqual( feature.qualifiers["description"], "EXTRACELLULAR (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[1] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 19) self.assertEqual(feature.location.end, 40) self.assertEqual(feature.qualifiers["description"], "1 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[2] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 40) self.assertEqual(feature.location.end, 58) self.assertEqual(feature.qualifiers["description"], "CYTOPLASMIC (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[3] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 58) self.assertEqual(feature.location.end, 79) self.assertEqual(feature.qualifiers["description"], "2 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[4] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 79) self.assertEqual(feature.location.end, 93) self.assertEqual( feature.qualifiers["description"], "EXTRACELLULAR (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[5] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 93) self.assertEqual(feature.location.end, 116) self.assertEqual(feature.qualifiers["description"], "3 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[6] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 116) self.assertEqual(feature.location.end, 137) self.assertEqual(feature.qualifiers["description"], "CYTOPLASMIC (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[7] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 137) self.assertEqual(feature.location.end, 158) self.assertEqual(feature.qualifiers["description"], "4 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[8] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 158) self.assertEqual(feature.location.end, 192) self.assertEqual( feature.qualifiers["description"], "EXTRACELLULAR (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[9] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 192) self.assertEqual(feature.location.end, 213) self.assertEqual(feature.qualifiers["description"], "5 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[10] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 213) self.assertEqual(feature.location.end, 260) self.assertEqual(feature.qualifiers["description"], "CYTOPLASMIC (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[11] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 260) self.assertEqual(feature.location.end, 281) self.assertEqual(feature.qualifiers["description"], "6 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[12] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 281) self.assertEqual(feature.location.end, 294) self.assertEqual( feature.qualifiers["description"], "EXTRACELLULAR (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[13] self.assertEqual(feature.type, "TRANSMEM") self.assertEqual(feature.location.start, 294) self.assertEqual(feature.location.end, 315) self.assertEqual(feature.qualifiers["description"], "7 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[14] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 315) self.assertEqual(feature.location.end, 388) self.assertEqual(feature.qualifiers["description"], "CYTOPLASMIC (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[15] 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[16] 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[17] self.assertEqual(feature.type, "LIPID") self.assertEqual(feature.location.start, 328) self.assertEqual(feature.location.end, 329) self.assertEqual( feature.qualifiers["description"], "PALMITATE (BY SIMILARITY)." ) self.assertIsNone(feature.id) feature = record.features[18] self.assertEqual(feature.type, "VARSPLIC") 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.assertIsNone(feature.id) feature = record.features[19] self.assertEqual(feature.type, "VARSPLIC") 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.assertIsNone(feature.id) feature = record.features[20] self.assertEqual(feature.type, "VARSPLIC") 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.assertIsNone(feature.id) feature = record.features[21] self.assertEqual(feature.type, "VARSPLIC") 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.assertIsNone(feature.id) feature = record.features[22] self.assertEqual(feature.type, "VARSPLIC") 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.assertIsNone(feature.id) self.assertEqual(len(record.references), 6) 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 receptor isoforms produced by alternative splicing in the carboxyl terminus.", ) self.assertEqual(len(record.references[0].references), 1) self.assertEqual(record.references[0].references[0], ("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), 1) self.assertEqual(record.references[2].references[0], ("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 receptors splice variants show marked constitutive activity: role of the c-terminal intracellular domain.", ) self.assertEqual(len(record.references[3].references), 0) self.assertEqual( record.references[4].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[4].title, "Structure of the human serotonin 5-HT4 receptor gene and cloning of a novel 5-HT4 splice variant.", ) self.assertEqual(len(record.references[4].references), 1) self.assertEqual(record.references[4].references[0], ("PubMed", "10646498")) self.assertEqual( record.references[5].authors, "Ullmer C., Schmuck K., Kalkman H.O., Lubbert H.", ) self.assertEqual( record.references[5].title, "Expression of serotonin receptor mRNAs in blood vessels.", ) self.assertEqual(len(record.references[5].references), 2) self.assertEqual(record.references[5].references[0], ("MEDLINE", "95385798")) self.assertEqual(record.references[5].references[1], ("PubMed", "7656980")) # Check the two parsers agree on the essentials self.assertEqual(str(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(str(records[0].seq), str(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" # this is a more recent version of the file sp010 above 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(str(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(str(records[0].seq), str(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_sp011(self): """Parsing SwissProt file sp011.""" filename = "sp011" # 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, "LUTROPIN-CHORIOGONADOTROPIC HORMONE RECEPTOR PRECURSOR (LH/CG-R) (LSH-R) (LUTEINIZING HORMONE RECEPTOR).", ) 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"] ) self.assertEqual( record.organism_classification, [ "Eukaryota", "Metazoa", "Chordata", "Craniata", "Vertebrata", "Euteleostomi", "Mammalia", "Eutheria", "Rodentia", "Sciurognathi", "Muridae", "Murinae", "Rattus", ], ) self.assertEqual(record.seqinfo, (700, 78035, "31807E73BAC94F1F")) self.assertEqual(len(record.features), 52) 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["description"], "") self.assertIsNone(feature.id) 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["description"], "LUTROPIN-CHORIOGONADOTROPIC HORMONE RECEPTOR.", ) self.assertIsNone(feature.id) feature = record.features[2] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 26) self.assertEqual(feature.location.end, 362) self.assertEqual( feature.qualifiers["description"], "EXTRACELLULAR (POTENTIAL)." ) self.assertIsNone(feature.id) 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["description"], "1 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[4] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 390) self.assertEqual(feature.location.end, 399) self.assertEqual(feature.qualifiers["description"], "CYTOPLASMIC (POTENTIAL).") self.assertIsNone(feature.id) 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["description"], "2 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[6] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 422) self.assertEqual(feature.location.end, 443) self.assertEqual( feature.qualifiers["description"], "EXTRACELLULAR (POTENTIAL)." ) self.assertIsNone(feature.id) 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["description"], "3 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[8] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 466) self.assertEqual(feature.location.end, 486) self.assertEqual(feature.qualifiers["description"], "CYTOPLASMIC (POTENTIAL).") self.assertIsNone(feature.id) 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["description"], "4 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[10] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 509) self.assertEqual(feature.location.end, 529) self.assertEqual( feature.qualifiers["description"], "EXTRACELLULAR (POTENTIAL)." ) self.assertIsNone(feature.id) 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["description"], "5 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[12] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 551) self.assertEqual(feature.location.end, 574) self.assertEqual(feature.qualifiers["description"], "CYTOPLASMIC (POTENTIAL).") self.assertIsNone(feature.id) 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["description"], "6 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[14] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 598) self.assertEqual(feature.location.end, 609) self.assertEqual( feature.qualifiers["description"], "EXTRACELLULAR (POTENTIAL)." ) self.assertIsNone(feature.id) 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["description"], "7 (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[16] self.assertEqual(feature.type, "DOMAIN") self.assertEqual(feature.location.start, 631) self.assertEqual(feature.location.end, 700) self.assertEqual(feature.qualifiers["description"], "CYTOPLASMIC (POTENTIAL).") self.assertIsNone(feature.id) feature = record.features[17] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 51) self.assertEqual(feature.location.end, 75) self.assertEqual(feature.qualifiers["description"], "LRR 1.") self.assertIsNone(feature.id) feature = record.features[18] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 125) self.assertEqual(feature.location.end, 150) self.assertEqual(feature.qualifiers["description"], "LRR 2.") self.assertIsNone(feature.id) feature = record.features[19] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 151) self.assertEqual(feature.location.end, 175) self.assertEqual(feature.qualifiers["description"], "LRR 3.") self.assertIsNone(feature.id) feature = record.features[20] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 175) self.assertEqual(feature.location.end, 200) self.assertEqual(feature.qualifiers["description"], "LRR 4.") self.assertIsNone(feature.id) feature = record.features[21] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 201) self.assertEqual(feature.location.end, 224) self.assertEqual(feature.qualifiers["description"], "LRR 5.") self.assertIsNone(feature.id) feature = record.features[22] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 224) self.assertEqual(feature.location.end, 248) self.assertEqual(feature.qualifiers["description"], "LRR 6.") self.assertIsNone(feature.id) feature = record.features[23] self.assertEqual(feature.type, "REPEAT") self.assertEqual(feature.location.start, 249) self.assertEqual(feature.location.end, 271) self.assertEqual(feature.qualifiers["description"], "LRR 7.") self.assertIsNone(feature.id) feature = record.features[24] self.assertEqual(feature.type, "DISULFID") self.assertEqual(feature.location.start, 442) self.assertEqual(feature.location.end, 518) self.assertEqual(feature.qualifiers["description"], "BY SIMILARITY.") self.assertIsNone(feature.id) feature = record.features[25] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 102) self.assertEqual(feature.location.end, 103) self.assertEqual( feature.qualifiers["description"], "N-LINKED (GLCNAC...) (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[26] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 177) self.assertEqual(feature.location.end, 178) self.assertEqual( feature.qualifiers["description"], "N-LINKED (GLCNAC...) (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[27] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 198) self.assertEqual(feature.location.end, 199) self.assertEqual( feature.qualifiers["description"], "N-LINKED (GLCNAC...) (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[28] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 294) self.assertEqual(feature.location.end, 295) self.assertEqual( feature.qualifiers["description"], "N-LINKED (GLCNAC...) (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[29] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 302) self.assertEqual(feature.location.end, 303) self.assertEqual( feature.qualifiers["description"], "N-LINKED (GLCNAC...) (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[30] self.assertEqual(feature.type, "CARBOHYD") self.assertEqual(feature.location.start, 316) self.assertEqual(feature.location.end, 317) self.assertEqual( feature.qualifiers["description"], "N-LINKED (GLCNAC...) (POTENTIAL)." ) self.assertIsNone(feature.id) feature = record.features[31] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 82) self.assertEqual(feature.location.end, 132) self.assertEqual( feature.qualifiers["description"], "MISSING (IN ISOFORM 1950)." ) self.assertIsNone(feature.id) feature = record.features[32] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 132) self.assertEqual(feature.location.end, 157) self.assertEqual( feature.qualifiers["description"], "MISSING (IN ISOFORM 1759)." ) self.assertIsNone(feature.id) feature = record.features[33] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 183) self.assertEqual(feature.location.end, 700) self.assertEqual(feature.qualifiers["description"], "MISSING (IN ISOFORM C2).") self.assertIsNone(feature.id) feature = record.features[34] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 231) self.assertEqual(feature.location.end, 251) self.assertEqual( feature.qualifiers["description"], "DISSTKLQALPSHGLESIQT -> PCRATGWSPFRRSSPCLPTH (IN ISOFORM 2075).", ) self.assertIsNone(feature.id) feature = record.features[35] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 231) self.assertEqual(feature.location.end, 293) self.assertEqual( feature.qualifiers["description"], "MISSING (IN ISOFORM E/A2, ISOFORM EB AND ISOFORM B1).", ) self.assertIsNone(feature.id) feature = record.features[36] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 251) self.assertEqual(feature.location.end, 700) self.assertEqual( feature.qualifiers["description"], "MISSING (IN ISOFORM 2075)." ) self.assertIsNone(feature.id) feature = record.features[37] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 293) self.assertEqual(feature.location.end, 367) self.assertEqual( feature.qualifiers["description"], "QNFSFSIFENFSKQCESTVRKADNETLYSAIFEENELSGWDYDYGFCSPKTLQCAPEPDAFNPCEDIMGYAFLR -> IFHFPFLKTSPNNAKAQLEKQITRRFIPPSLRRMNSVAGIMIMASVHPRHSNVLQNQMLSTPVKILWAMPSLGS (IN ISOFORM B1 AND ISOFORM B3).", ) self.assertIsNone(feature.id) feature = record.features[38] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 293) self.assertEqual(feature.location.end, 294) self.assertEqual(feature.qualifiers["description"], "Q -> P (IN ISOFORM C1).") self.assertIsNone(feature.id) feature = record.features[39] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 294) self.assertEqual(feature.location.end, 700) self.assertEqual(feature.qualifiers["description"], "MISSING (IN ISOFORM C1).") self.assertIsNone(feature.id) feature = record.features[40] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 320) self.assertEqual(feature.location.end, 342) self.assertEqual( feature.qualifiers["description"], "YSAIFEENELSGWDYDYGFCSP -> LHGALPAAHCLRGLPNKRPVL (IN ISOFORM 1834, ISOFORM 1759 AND ISOFORM EB).", ) self.assertIsNone(feature.id) feature = record.features[41] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 342) self.assertEqual(feature.location.end, 700) self.assertEqual( feature.qualifiers["description"], "MISSING (IN ISOFORMS 1834, ISOFORM 1759 AND ISOFORM EB).", ) self.assertIsNone(feature.id) feature = record.features[42] self.assertEqual(feature.type, "VARSPLIC") self.assertEqual(feature.location.start, 367) self.assertEqual(feature.location.end, 700) self.assertEqual( feature.qualifiers["description"], "MISSING (IN ISOFORM B1 AND ISOFORM B3)." ) self.assertIsNone(feature.id) feature = record.features[43] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 81) self.assertEqual(feature.location.end, 82) self.assertEqual(feature.qualifiers["description"], "I -> M (IN ISOFORM 1950).") self.assertIsNone(feature.id) feature = record.features[44] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 178) self.assertEqual(feature.location.end, 179) self.assertEqual(feature.qualifiers["description"], "E -> G (IN ISOFORM 1759).") self.assertIsNone(feature.id) feature = record.features[45] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 232) self.assertEqual(feature.location.end, 233) self.assertEqual(feature.qualifiers["description"], "I -> T (IN ISOFORM 1950).") self.assertIsNone(feature.id) feature = record.features[46] self.assertEqual(feature.type, "VARIANT") self.assertEqual(feature.location.start, 645) self.assertEqual(feature.location.end, 646) self.assertEqual(feature.qualifiers["description"], "G -> S (IN ISOFORM 1950).") self.assertIsNone(feature.id) feature = record.features[47] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 408) self.assertEqual(feature.location.end, 409) self.assertEqual( feature.qualifiers["description"], "D->N: SIGNIFICANT REDUCTION OF BINDING." ) self.assertIsNone(feature.id) feature = record.features[48] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 435) self.assertEqual(feature.location.end, 436) self.assertEqual( feature.qualifiers["description"], "D->N: NO CHANGE IN BINDING OR CAMP PROD.", ) self.assertIsNone(feature.id) feature = record.features[49] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 454) self.assertEqual(feature.location.end, 455) self.assertEqual( feature.qualifiers["description"], "E->Q: NO CHANGE IN BINDING OR CAMP PROD.", ) self.assertIsNone(feature.id) feature = record.features[50] self.assertEqual(feature.type, "MUTAGEN") self.assertEqual(feature.location.start, 581) self.assertEqual(feature.location.end, 582) self.assertEqual( feature.qualifiers["description"], "D->N: NO CHANGE IN BINDING OR CAMP PROD.", ) self.assertIsNone(feature.id) feature = record.features[51] self.assertEqual(feature.type, "CONFLICT") self.assertEqual(feature.location.start, 32) self.assertEqual(feature.location.end, 33) self.assertEqual(feature.qualifiers["description"], "R -> L (IN REF. 7).") self.assertIsNone(feature.id) self.assertEqual(len(record.references), 8) self.assertEqual( record.references[0].authors, "McFarland K.C., Sprengel R., Phillips H.S., Koehler M., Rosemblit N., Nikolics K., Segaloff D.L., Seeburg P.H.", ) self.assertEqual( record.references[0].title, "Lutropin-choriogonadotropin receptor: an unusual member of the G protein-coupled receptor family.", ) self.assertEqual(len(record.references[0].references), 2) self.assertEqual(record.references[0].references[0], ("MEDLINE", "89332512")) self.assertEqual(record.references[0].references[1], ("PubMed", "2502842")) self.assertEqual( record.references[1].authors, "Aatsinki J.T., Pietila E.M., Lakkakorpi J.T., Rajaniemi H.J.", ) self.assertEqual( record.references[1].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(record.references[1].references), 2) self.assertEqual(record.references[1].references[0], ("MEDLINE", "92347604")) self.assertEqual(record.references[1].references[1], ("PubMed", "1353463")) self.assertEqual( record.references[2].authors, "Koo Y.B., Slaughter R.G., Ji T.H." ) self.assertEqual( record.references[2].title, "Structure of the luteinizing hormone receptor gene and multiple exons of the coding sequence.", ) self.assertEqual(len(record.references[2].references), 2) self.assertEqual(record.references[2].references[0], ("MEDLINE", "91209270")) self.assertEqual(record.references[2].references[1], ("PubMed", "2019252")) self.assertEqual( record.references[3].authors, "Bernard M.P., Myers R.V., Moyle W.R." ) self.assertEqual( record.references[3].title, "Cloning of rat lutropin (LH) receptor analogs lacking the soybean lectin domain.", ) self.assertEqual(len(record.references[3].references), 2) self.assertEqual(record.references[3].references[0], ("MEDLINE", "91006819")) self.assertEqual(record.references[3].references[1], ("PubMed", "1976554")) self.assertEqual( record.references[4].authors, "Segaloff D.L., Sprengel R., Nikolics K., Ascoli M.", ) self.assertEqual( record.references[4].title, "Structure of the lutropin/choriogonadotropin receptor.", ) self.assertEqual(len(record.references[4].references), 2) self.assertEqual(record.references[4].references[0], ("MEDLINE", "91126285")) self.assertEqual(record.references[4].references[1], ("PubMed", "2281186")) self.assertEqual( record.references[5].authors, "Tsai-Morris C.H., Buczko E., Wang W., Dufau M.L.", ) self.assertEqual( record.references[5].title, "Intronic nature of the rat luteinizing hormone receptor gene defines a soluble receptor subspecies with hormone binding activity.", ) self.assertEqual(len(record.references[5].references), 2) self.assertEqual(record.references[5].references[0], ("MEDLINE", "91060531")) self.assertEqual(record.references[5].references[1], ("PubMed", "2174034")) self.assertEqual(record.references[6].authors, "Roche P.C., Ryan R.J.") self.assertEqual( record.references[6].title, "Purification, characterization, and amino-terminal sequence of rat ovarian receptor for luteinizing hormone/human choriogonadotropin.", ) self.assertEqual(len(record.references[6].references), 2) self.assertEqual(record.references[6].references[0], ("MEDLINE", "89174723")) self.assertEqual(record.references[6].references[1], ("PubMed", "2925659")) self.assertEqual(record.references[7].authors, "Ji I., Ji T.H.") self.assertEqual( record.references[7].title, "Asp383 in the second transmembrane domain of the lutropin receptor is important for high affinity hormone binding and cAMP production.", ) self.assertEqual(len(record.references[7].references), 2) self.assertEqual(record.references[7].references[0], ("MEDLINE", "91332007")) self.assertEqual(record.references[7].references[1], ("PubMed", "1714448")) # Check the two parsers agree on the essentials self.assertEqual(str(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(str(records[0].seq), str(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(str(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(str(records[0].seq), str(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(str(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(str(records[0].seq), str(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(str(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(str(records[0].seq), str(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(str(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(str(records[0].seq), str(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_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)