#!/usr/bin/env python # 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 # Left as None if the import within UniProtIO fails if SeqIO.UniprotIO.ElementTree is None: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError("No ElementTree module was found. " "Use Python 2.5+, lxml or elementtree " "if you want to use " "Bio.SeqIO.UniprotIO.") from seq_tests_common import compare_reference, compare_record class TestUniprot(unittest.TestCase): def test_uni001(self): "Parsing Uniprot file uni001" filename = 'uni001' # test the record parser datafile = os.path.join('SwissProt', filename) with open(datafile) as test_handle: seq_record = SeqIO.read(test_handle, "uniprot-xml") self.assertTrue(isinstance(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', ProteinAlphabet())") # 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) test_handle = open(datafile) seq_record = SeqIO.read(test_handle, "uniprot-xml") test_handle.close() self.assertTrue(isinstance(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('MMTSLLTISMFVVAIQAFDSSEIRMLDEQYDTKNPFFQF" "LENSKRSDRPTRAMD...GRK', ProteinAlphabet())") 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) test_handle = open(datafile) seq_record = SeqIO.read(test_handle, "swiss") test_handle.close() self.assertTrue(isinstance(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) test_handle = open(datafile) seq_record = SeqIO.read(test_handle, "swiss") test_handle.close() self.assertTrue(isinstance(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): 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 genem 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).""" for entry in SeqIO.parse(open("SwissProt/R5HY77.xml"), "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)