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#!/usr/bin/env python
"""Test for the Uniprot parser on Uniprot XML files.
"""
import os
import copy
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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "uniprot-xml")
test_handle.close()
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 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 MXL? 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 type(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_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"))
ids = [x.strip() for x in open("SwissProt/multi_ex.list")]
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.assertTrue(txt.id in 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"))
ids = [x.strip() for x in open("SwissProt/multi_ex.list")]
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)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
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