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test_Uniprot.py

#!/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

00020 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))

00133     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)
    
00139     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)
    
00154     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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