# Copyright 2010 by Andrea Pierleoni # Revisions copyright 2010-2015 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 Uniprot parser on Uniprot XML files.""" import os import unittest from Bio import SeqIO from Bio.SeqRecord import SeqRecord from seq_tests_common import compare_reference, compare_record class TestUniprot(unittest.TestCase): """Tests Uniprot XML parser.""" def test_uni001(self): """Parsing Uniprot file uni001.""" filename = "uni001" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as handle: seq_record = SeqIO.read(handle, "uniprot-xml") self.assertIsInstance(seq_record, SeqRecord) # test a couple of things on the record -- this is not exhaustive self.assertEqual(seq_record.id, "Q91G55") self.assertEqual(seq_record.name, "043L_IIV6") self.assertEqual(seq_record.description, "Uncharacterized protein 043L") self.assertEqual( repr(seq_record.seq), "Seq('MDLINNKLNIEIQKFCLDLEKKYNINYNNLIDLWFNKESTERLIKCEVNLENKI...IPI')", ) # self.assertEqual(seq_record.accessions, ['Q91G55']) #seq_record.accessions does not exist # self.assertEqual(seq_record.organism_classification, ['Eukaryota', 'Metazoa', 'Chordata', 'Craniata', 'Vertebrata', 'Mammalia', 'Eutheria', 'Primates', 'Catarrhini', 'Hominidae', 'Homo']) # self.assertEqual(record.seqinfo, (348, 39676, '75818910')) self.assertEqual(len(seq_record.features), 1) self.assertEqual( repr(seq_record.features[0]), "SeqFeature(FeatureLocation(ExactPosition(0), ExactPosition(116)), type='chain', id='PRO_0000377969')", ) self.assertEqual(len(seq_record.annotations["references"]), 2) self.assertEqual( seq_record.annotations["references"][0].authors, "Jakob N.J., Mueller K., Bahr U., Darai G.", ) self.assertEqual( seq_record.annotations["references"][0].title, "Analysis of the first complete DNA sequence of an invertebrate iridovirus: coding strategy of the genome of Chilo iridescent virus.", ) self.assertEqual( seq_record.annotations["references"][0].journal, "Virology 286:182-196(2001)", ) self.assertEqual( seq_record.annotations["references"][0].comment, "journal article | 2001 | Scope: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] | ", ) self.assertEqual(len(seq_record.dbxrefs), 11) self.assertEqual(seq_record.dbxrefs[0], "DOI:10.1006/viro.2001.0963") self.assertEqual(seq_record.annotations["sequence_length"], 116) self.assertEqual( seq_record.annotations["sequence_checksum"], "4A29B35FB716523C" ) self.assertEqual(seq_record.annotations["modified"], "2009-07-07") self.assertEqual(seq_record.annotations["accessions"], ["Q91G55"]) self.assertEqual( seq_record.annotations["taxonomy"], ["Viruses", "dsDNA viruses, no RNA stage", "Iridoviridae", "Iridovirus"], ) self.assertEqual(seq_record.annotations["sequence_mass"], 13673) self.assertEqual(seq_record.annotations["dataset"], "Swiss-Prot") self.assertEqual(seq_record.annotations["gene_name_ORF"], ["IIV6-043L"]) self.assertEqual(seq_record.annotations["version"], 21) self.assertEqual(seq_record.annotations["sequence_modified"], "2001-12-01") self.assertEqual( seq_record.annotations["keywords"], ["Complete proteome", "Virus reference strain"], ) self.assertEqual( seq_record.annotations["organism_host"], [ "Acheta domesticus", "House cricket", "Chilo suppressalis", "striped riceborer", "Gryllus bimaculatus", "Two-spotted cricket", "Gryllus campestris", "Spodoptera frugiperda", "Fall armyworm", ], ) self.assertEqual(seq_record.annotations["created"], "2009-06-16") self.assertEqual( seq_record.annotations["organism_name"], ["Chilo iridescent virus"] ) self.assertEqual( seq_record.annotations["organism"], "Invertebrate iridescent virus 6 (IIV-6)", ) self.assertEqual( seq_record.annotations["recommendedName_fullName"], ["Uncharacterized protein 043L"], ) self.assertEqual(seq_record.annotations["sequence_version"], 1) self.assertEqual(seq_record.annotations["proteinExistence"], ["Predicted"]) def test_uni003(self): """Parsing Uniprot file uni003.""" filename = "uni003" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as handle: seq_record = SeqIO.read(handle, "uniprot-xml") self.assertIsInstance(seq_record, SeqRecord) # test general record entries self.assertEqual(seq_record.id, "O44185") self.assertEqual(seq_record.name, "FLP13_CAEEL") self.assertEqual(seq_record.description, "FMRFamide-like neuropeptides 13") self.assertEqual( repr(seq_record.seq), "Seq('MMTSLLTISMFVVAIQAFDSSEIRMLDEQYDTKNPFFQFLENSKRSDRPTRAMD...GRK')", ) self.assertEqual(len(seq_record.annotations["references"]), 7) self.assertEqual( seq_record.annotations["references"][5].authors, "Kim K., Li C." ) self.assertEqual( seq_record.annotations["references"][5].title, "Expression and regulation of an FMRFamide-related " "neuropeptide gene family in Caenorhabditis elegans.", ) self.assertEqual( seq_record.annotations["references"][5].journal, "J. Comp. Neurol. 475:540-550(2004)", ) self.assertEqual( seq_record.annotations["references"][5].comment, "journal article | 2004 | Scope: TISSUE SPECIFICITY, " "DEVELOPMENTAL STAGE | ", ) self.assertEqual(seq_record.annotations["accessions"], ["O44185"]) self.assertEqual(seq_record.annotations["created"], "2004-05-10") self.assertEqual(seq_record.annotations["dataset"], "Swiss-Prot") self.assertEqual(seq_record.annotations["gene_name_ORF"], ["F33D4.3"]) self.assertEqual(seq_record.annotations["gene_name_primary"], "flp-13") self.assertEqual( seq_record.annotations["keywords"], [ "Amidation", "Cleavage on pair of basic residues", "Complete proteome", "Direct protein sequencing", "Neuropeptide", "Reference proteome", "Repeat", "Secreted", "Signal", ], ) self.assertEqual(seq_record.annotations["modified"], "2012-11-28") self.assertEqual(seq_record.annotations["organism"], "Caenorhabditis elegans") self.assertEqual( seq_record.annotations["proteinExistence"], ["evidence at protein level"] ) self.assertEqual( seq_record.annotations["recommendedName_fullName"], ["FMRFamide-like neuropeptides 13"], ) self.assertEqual(seq_record.annotations["sequence_length"], 160) self.assertEqual( seq_record.annotations["sequence_checksum"], "BE4C24E9B85FCD11" ) self.assertEqual(seq_record.annotations["sequence_mass"], 17736) self.assertEqual(seq_record.annotations["sequence_modified"], "1998-06-01") self.assertEqual(seq_record.annotations["sequence_precursor"], "true") self.assertEqual(seq_record.annotations["sequence_version"], 1) self.assertEqual( seq_record.annotations["taxonomy"], [ "Eukaryota", "Metazoa", "Ecdysozoa", "Nematoda", "Chromadorea", "Rhabditida", "Rhabditoidea", "Rhabditidae", "Peloderinae", "Caenorhabditis", ], ) self.assertEqual(seq_record.annotations["type"], ["ECO:0000006", "ECO:0000001"]) self.assertEqual(seq_record.annotations["version"], 74) # test comment entries self.assertEqual( seq_record.annotations["comment_allergen"], ["Causes an allergic reaction in human."], ) self.assertEqual( seq_record.annotations["comment_alternativeproducts_isoform"], ["Q8W1X2-1", "Q8W1X2-2"], ) self.assertEqual( seq_record.annotations["comment_biotechnology"], [ "Green fluorescent protein has been engineered to " "produce a vast number of variously colored " "mutants, fusion proteins, and biosensors. " "Fluorescent proteins and its mutated allelic " "forms, blue, cyan and yellow have become a useful " "and ubiquitous tool for making chimeric proteins, " "where they function as a fluorescent protein tag. " "Typically they tolerate N- and C-terminal fusion " "to a broad variety of proteins. They have been " "expressed in most known cell types and are used " "as a noninvasive fluorescent marker in living " "cells and organisms. They enable a wide range of " "applications where they have functioned as a cell " "lineage tracer, reporter of gene expression, or as " "a measure of protein-protein interactions.", "Can also be used as a molecular thermometer, " "allowing accurate temperature measurements in " "fluids. The measurement process relies on the " "detection of the blinking of GFP using " "fluorescence correlation spectroscopy.", ], ) self.assertEqual( seq_record.annotations["comment_catalyticactivity"], [ "ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA.", "ATP + biotin-[carboxyl-carrier-protein] " "+ CO(2) = ADP + phosphate + " "carboxy-biotin-[carboxyl-carrier-protein].", ], ) self.assertEqual( seq_record.annotations["comment_caution"], [ "Could be the product of a pseudogene. The " "existence of a transcript at this locus is " "supported by only one sequence submission " "(PubMed:2174397)." ], ) self.assertEqual( seq_record.annotations["comment_cofactor"], [ "Biotin (By similarity).", "Binds 2 manganese ions per subunit (By similarity).", ], ) self.assertEqual( seq_record.annotations["comment_developmentalstage"], [ "Expressed from the comma stage of embryogenesis, " "during all larval stages, and in low levels in " "adults." ], ) self.assertEqual( seq_record.annotations["comment_disease"], [ "Defects in MC2R are the cause of glucocorticoid " "deficiency type 1 (GCCD1) [MIM:202200]; also known " "as familial glucocorticoid deficiency type 1 " "(FGD1). GCCD1 is an autosomal recessive disorder " "due to congenital insensitivity or resistance to " "adrenocorticotropin (ACTH). It is characterized by " "progressive primary adrenal insufficiency, without " "mineralocorticoid deficiency." ], ) self.assertEqual( seq_record.annotations["comment_disruptionphenotype"], [ "Mice display impaired B-cell development which " "does not progress pass the progenitor stage." ], ) self.assertEqual( seq_record.annotations["comment_domain"], [ "Two regions, an N-terminal (aa 96-107) and a " "C-terminal (aa 274-311) are required for binding " "FGF2." ], ) self.assertEqual( seq_record.annotations["comment_enzymeregulation"], [ "By phosphorylation. The catalytic activity is " "inhibited by soraphen A, a polyketide isolated " "from the myxobacterium Sorangium cellulosum and " "a potent inhibitor of fungal growth." ], ) self.assertEqual( seq_record.annotations["comment_function"], [ "FMRFamides and FMRFamide-like peptides are " "neuropeptides. AADGAPLIRF-amide and " "APEASPFIRF-amide inhibit muscle tension in somatic " "muscle. APEASPFIRF-amide is a potent inhibitor of " "the activity of dissected pharyngeal myogenic " "muscle system." ], ) self.assertEqual( seq_record.annotations["comment_induction"], [ "Repressed in presence of fatty acids. Repressed " "3-fold by lipid precursors, inositol and " "choline, and also controlled by regulatory " "factors INO2, INO4 and OPI1." ], ) self.assertEqual( seq_record.annotations["comment_interaction_intactId"], ["EBI-356720", "EBI-746969", "EBI-720116"], ) self.assertEqual( seq_record.annotations["comment_massspectrometry"], ["88..98:1032|MALDI", "100..110:1133.7|MALDI"], ) self.assertEqual( seq_record.annotations["comment_miscellaneous"], ["Present with 20200 molecules/cell in log phase SD medium."], ) self.assertEqual( seq_record.annotations["comment_onlineinformation"], ["NIEHS-SNPs@http://egp.gs.washington.edu/data/api5/"], ) self.assertEqual( seq_record.annotations["comment_pathway"], [ "Lipid metabolism; malonyl-CoA biosynthesis; " "malonyl-CoA from acetyl-CoA: step 1/1." ], ) self.assertEqual( seq_record.annotations["comment_RNAediting"], [ "Partially edited. RNA editing generates receptor " "isoforms that differ in their ability to interact " "with the phospholipase C signaling cascade in a " "transfected cell line, suggesting that this RNA " "processing event may contribute to the modulation " "of serotonergic neurotransmission in the central " "nervous system." ], ) self.assertEqual( seq_record.annotations["comment_PTM"], ["Acetylation at Lys-251 impairs antiapoptotic function."], ) self.assertEqual( seq_record.annotations["comment_pharmaceutical"], [ "Could be used as a possible therapeutic agent for " "treating rheumatoid arthritis." ], ) self.assertEqual( seq_record.annotations["comment_polymorphism"], [ "Position 23 is polymorphic; the frequencies in " "unrelated Caucasians are 0.87 for Cys and 0.13 " "for Ser." ], ) self.assertEqual( seq_record.annotations["comment_similarity"], ["Belongs to the FARP (FMRFamide related peptide) family."], ) self.assertEqual( seq_record.annotations["comment_subcellularlocation_location"], ["Secreted"] ) self.assertEqual(seq_record.annotations["comment_subunit"], ["Homodimer."]) self.assertEqual( seq_record.annotations["comment_tissuespecificity"], [ "Each flp gene is expressed in a distinct set of " "neurons. Flp-13 is expressed in the ASE sensory " "neurons, the DD motor neurons, the 15, M3 and M5 " "cholinergic pharyngeal motoneurons, and the ASG, " "ASK and BAG neurons." ], ) self.assertEqual( seq_record.annotations["comment_toxicdose"], [ "LD(50) is 50 ug/kg in mouse by " "intracerebroventricular injection " "and 600 ng/g in Blatella germanica." ], ) def test_sp016(self): """Parsing SwissProt file sp016.""" filename = "sp016" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as handle: seq_record = SeqIO.read(handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) # test ProteinExistence (the numerical value describing the evidence for the existence of the protein) self.assertEqual(seq_record.annotations["protein_existence"], 1) # test Sequence version self.assertEqual(seq_record.annotations["sequence_version"], 1) # test Entry version self.assertEqual(seq_record.annotations["entry_version"], 93) def test_sp002(self): """Parsing SwissProt file sp002.""" filename = "sp002" # test the record parser datafile = os.path.join("SwissProt", filename) with open(datafile) as handle: seq_record = SeqIO.read(handle, "swiss") self.assertIsInstance(seq_record, SeqRecord) # test Sequence version self.assertEqual(seq_record.annotations["sequence_version"], 34) # test Entry version self.assertEqual(seq_record.annotations["entry_version"], 36) def compare_txt_xml(self, old, new): """Compare text and XML based parser output.""" self.assertEqual(old.id, new.id) self.assertEqual(old.name, new.name) self.assertEqual(len(old), len(new)) self.assertEqual(str(old.seq), str(new.seq)) for key in set(old.annotations).intersection(new.annotations): if key == "references": self.assertEqual(len(old.annotations[key]), len(new.annotations[key])) for r1, r2 in zip(old.annotations[key], new.annotations[key]): # Tweak for line breaks in plain text SwissProt r1.title = r1.title.replace("- ", "-") r2.title = r2.title.replace("- ", "-") r1.journal = r1.journal.rstrip(".") # Should parser do this? r1.medline_id = "" # Missing in UniPort XML? TODO - check # Lots of extra comments in UniProt XML r1.comment = "" r2.comment = "" if not r2.journal: r1.journal = "" compare_reference(r1, r2) elif old.annotations[key] == new.annotations[key]: pass elif key in ["date"]: # TODO - Why is this a list vs str? pass elif not isinstance(old.annotations[key], type(new.annotations[key])): raise TypeError( "%s gives %s vs %s" % (key, old.annotations[key], new.annotations[key]) ) elif key in ["organism"]: if old.annotations[key] == new.annotations[key]: pass elif old.annotations[key].startswith(new.annotations[key] + " "): pass else: raise ValueError(key) elif isinstance(old.annotations[key], list) and sorted( old.annotations[key] ) == sorted(new.annotations[key]): pass else: raise ValueError( "%s gives %s vs %s" % (key, old.annotations[key], new.annotations[key]) ) self.assertEqual( len(old.features), len(new.features), "Features in %s, %i vs %i" % (old.id, len(old.features), len(new.features)), ) for f1, f2 in zip(old.features, new.features): """ self.assertEqual(f1.location.nofuzzy_start, f2.location.nofuzzy_start, "%s %s vs %s %s" % (f1.location, f1.type, f2.location, f2.type)) self.assertEqual(f1.location.nofuzzy_end, f2.location.nofuzzy_end, "%s %s vs %s %s" % (f1.location, f1.type, f2.location, f2.type)) """ self.assertEqual( repr(f1.location), repr(f2.location), "%s %s vs %s %s" % (f1.location, f1.type, f2.location, f2.type), ) def test_Q13639(self): """Compare SwissProt text and uniprot XML versions of Q13639.""" old = SeqIO.read("SwissProt/Q13639.txt", "swiss") new = SeqIO.read("SwissProt/Q13639.xml", "uniprot-xml") self.compare_txt_xml(old, new) def test_H2CNN8(self): """Compare SwissProt text and uniprot XML versions of H2CNN8.""" old = SeqIO.read("SwissProt/H2CNN8.txt", "swiss") new = SeqIO.read("SwissProt/H2CNN8.xml", "uniprot-xml") self.compare_txt_xml(old, new) def test_F2CXE6(self): """Compare SwissProt text and uniprot XML versions of F2CXE6.""" # This evil record has a semi-colon in the gene name, # GN Name=HvPIP2;8 {ECO:0000313|EMBL:BAN04711.1}; # HvPIP2;8 old = SeqIO.read("SwissProt/F2CXE6.txt", "swiss") new = SeqIO.read("SwissProt/F2CXE6.xml", "uniprot-xml") self.compare_txt_xml(old, new) # TODO - Why the mismatch gene_name vs gene_name_primary? # TODO - Handle evidence codes on GN line (see GitHub isse #416) self.assertEqual( old.annotations["gene_name"], "Name=HvPIP2;8 {ECO:0000313|EMBL:BAN04711.1};" ) self.assertEqual(new.annotations["gene_name_primary"], "HvPIP2;8") self.assertEqual(old.name, "F2CXE6_HORVD") self.assertEqual(new.name, "F2CXE6_HORVD") def test_P84001(self): """Parse mass spec structured comment with unknown loc.""" xml = list(SeqIO.parse("SwissProt/P84001.xml", "uniprot-xml"))[0] self.assertEqual(xml.id, "P84001") self.assertEqual(len(xml.annotations["comment_massspectrometry"]), 1) self.assertEqual( xml.annotations["comment_massspectrometry"][0], "undefined:9571|Electrospray", ) def test_multi_ex(self): """Compare SwissProt text and uniprot XML versions of several examples.""" txt_list = list(SeqIO.parse("SwissProt/multi_ex.txt", "swiss")) xml_list = list(SeqIO.parse("SwissProt/multi_ex.xml", "uniprot-xml")) fas_list = list(SeqIO.parse("SwissProt/multi_ex.fasta", "fasta")) with open("SwissProt/multi_ex.list") as handle: ids = [x.strip() for x in handle] self.assertEqual(len(txt_list), len(ids)) self.assertEqual(len(txt_list), len(fas_list)) self.assertEqual(len(txt_list), len(xml_list)) for txt, xml, fas, id in zip(txt_list, xml_list, fas_list, ids): self.assertEqual(txt.id, id) self.assertIn(txt.id, fas.id.split("|")) self.assertEqual(str(txt.seq), str(fas.seq)) self.compare_txt_xml(txt, xml) def test_multi_ex_index(self): """Index SwissProt text and uniprot XML versions of several examples.""" txt_list = list(SeqIO.parse("SwissProt/multi_ex.txt", "swiss")) xml_list = list(SeqIO.parse("SwissProt/multi_ex.xml", "uniprot-xml")) with open("SwissProt/multi_ex.list") as handle: ids = [x.strip() for x in handle] txt_index = SeqIO.index("SwissProt/multi_ex.txt", "swiss") xml_index = SeqIO.index("SwissProt/multi_ex.xml", "uniprot-xml") self.assertEqual(sorted(txt_index), sorted(ids)) self.assertEqual(sorted(xml_index), sorted(ids)) # Check SeqIO.parse() versus SeqIO.index() for plain text "swiss" for old in txt_list: new = txt_index[old.id] compare_record(old, new) # Check SeqIO.parse() versus SeqIO.index() for XML "uniprot-xml" for old in xml_list: new = xml_index[old.id] compare_record(old, new) txt_index.close() xml_index.close() def test_submittedName_allowed(self): """Checks if parser supports new XML Element (submittedName).""" with open("SwissProt/R5HY77.xml") as handle: for entry in SeqIO.parse(handle, "uniprot-xml"): self.assertEqual(entry.id, "R5HY77") self.assertEqual(entry.description, "Elongation factor Ts") if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)