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test_SwissProt.py
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test_SwissProt.py
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#!/usr/bin/env python
"""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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
self.assert_(isinstance(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', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# 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)
self.assertEqual(record.features[0], ('TRANSMEM', 20, 40, 'POTENTIAL.', ''))
self.assertEqual(record.features[1], ('TRANSMEM', 197, 217, 'POTENTIAL.', ''))
self.assertEqual(record.features[2], ('TRANSMEM', 222, 242, 'POTENTIAL.', ''))
self.assertEqual(record.features[3], ('TRANSMEM', 277, 297, 'POTENTIAL.', ''))
self.assertEqual(record.features[4], ('TRANSMEM', 313, 333, 'POTENTIAL.', ''))
self.assertEqual(record.features[5], ('VARSPLIC', 344, 348, 'DLDFE -> FLIK (IN FORM 2).', ''))
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 the two parsers agree on the essentials
self.assertEqual(seq_record.seq.tostring(), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assert_(seq_record.id in record.accessions)
#Now try using the iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(records[0], SeqRecord))
#Check matches what we got earlier without the iterator:
self.assertEqual(records[0].seq.tostring(), seq_record.seq.tostring())
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
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
self.assert_(isinstance(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', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# 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)
self.assertEqual(record.features[0], ('DOMAIN', 13, 82, 'DNAJ-LIKE.', ''))
self.assertEqual(record.features[1], ('DOMAIN', 118, 128, 'POLY-CYS.', ''))
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(seq_record.seq.tostring(), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assert_(seq_record.id in record.accessions)
#Now try using the iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(records[0], SeqRecord))
#Check matches what we got earlier without the iterator:
self.assertEqual(records[0].seq.tostring(), seq_record.seq.tostring())
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
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
self.assert_(isinstance(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', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# 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)
self.assertEqual(record.features[0], ('MOD_RES', 1, 1, 'ACETYLATION.', ''))
self.assertEqual(record.features[1], ('CONFLICT', 73, 73, 'K -> T (IN REF. 8).', ''))
self.assertEqual(record.features[2], ('CONFLICT', 120, 120, 'F -> S (IN REF. 8).', ''))
self.assertEqual(record.features[3], ('CONFLICT', 123, 123, 'K -> Y (IN REF. 8).', ''))
self.assertEqual(record.features[4], ('CONFLICT', 129, 129, 'H -> Y (IN REF. 13).', ''))
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(seq_record.seq.tostring(), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assert_(seq_record.id in record.accessions)
#Now try using the iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(records[0], SeqRecord))
#Check matches what we got earlier without the iterator:
self.assertEqual(records[0].seq.tostring(), seq_record.seq.tostring())
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
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(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_sp004(self):
"Parsing SwissProt file sp004"
filename = 'sp004'
# 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.assert_(isinstance(seq_record, SeqRecord))
self.assertEqual(seq_record.id, "P23082")
self.assertEqual(seq_record.name, "NDOA_PSEPU")
self.assertEqual(seq_record.description, "NAPHTHALENE 1,2-DIOXYGENASE SYSTEM FERREDOXIN COMPONENT.")
self.assertEqual(repr(seq_record.seq), "Seq('TVKWIEAVALSDILEGDVLGVTVEGKELALYEVEGEIYATDNLCTHGSARMSDG...DLS', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# test a couple of things on the record -- this is not exhaustive
self.assertEqual(record.entry_name, "NDOA_PSEPU")
self.assertEqual(record.accessions, ['P23082', 'Q52123', 'O07829'])
self.assertEqual(record.organism_classification, ['Bacteria', 'Proteobacteria', 'gamma subdivision', 'Pseudomonas group', 'Pseudomonas'])
self.assertEqual(record.seqinfo, (103, 11315, '9F91B3C8'))
self.assertEqual(len(record.features), 12)
self.assertEqual(record.features[0], ('INIT_MET', 0, 0, '', ''))
self.assertEqual(record.features[1], ('METAL', 44, 44, 'IRON-SULFUR (2FE-2S) (POTENTIAL).', ''))
self.assertEqual(record.features[2], ('METAL', 46, 46, 'IRON-SULFUR (2FE-2S) (POTENTIAL).', ''))
self.assertEqual(record.features[3], ('METAL', 63, 63, 'IRON-SULFUR (2FE-2S) (POTENTIAL).', ''))
self.assertEqual(record.features[4], ('METAL', 66, 66, 'IRON-SULFUR (2FE-2S) (POTENTIAL).', ''))
self.assertEqual(record.features[5], ('VARIANT', 2, 2, 'V -> E (IN STRAIN G7).', ''))
self.assertEqual(record.features[6], ('VARIANT', 14, 14, 'L -> P (IN STRAIN G7).', ''))
self.assertEqual(record.features[7], ('VARIANT', 48, 48, 'S -> A (IN STRAIN G7).', ''))
self.assertEqual(record.features[8], ('VARIANT', 76, 76, 'K -> R (IN STRAIN G7).', ''))
self.assertEqual(record.features[9], ('VARIANT', 84, 84, 'Q -> E (IN STRAIN G7).', ''))
self.assertEqual(record.features[10], ('VARIANT', 90, 90, 'P -> A (IN STRAIN G7).', ''))
self.assertEqual(record.features[11], ('VARIANT', 103, 103, 'S -> GEF (IN STRAIN G7).', ''))
self.assertEqual(len(record.references), 4)
self.assertEqual(record.references[0].authors, "KURKELA S., LEHVAESLAIHO H., PALVA E.T., TEERI T.H.;")
self.assertEqual(record.references[0].title, '"Cloning, nucleotide sequence and characterization of genes encoding naphthalene dioxygenase of Pseudomonas putida strain NCIB9816.";')
self.assertEqual(len(record.references[0].references), 1)
self.assertEqual(record.references[0].references[0], ('MEDLINE', '89211973'))
self.assertEqual(record.references[1].authors, "SIMON M.J., OSSLUND T.D., SAUNDERS R., ENSLEY B.D., SUGGS S., HARCOURT A.A., SUEN W.-C., CRUDEN D.L., GIBSON D.T., ZYLSTRA G.J.;")
self.assertEqual(record.references[1].title, '"Sequences of genes encoding naphthalene dioxygenase in Pseudomonas putida strains G7 and NCIB 9816-4.";')
self.assertEqual(len(record.references[1].references), 1)
self.assertEqual(record.references[1].references[0], ('MEDLINE', '93252277'))
self.assertEqual(record.references[2].authors, "DENOME S.A., STANLEY D.C., OLSON E.S., YOUNG K.D.;")
self.assertEqual(record.references[2].title, '"Metabolism of dibenzothiophene and naphthalene in Pseudomonas strains: complete DNA sequence of an upper naphthalene catabolic pathway.";')
self.assertEqual(len(record.references[2].references), 1)
self.assertEqual(record.references[2].references[0], ('MEDLINE', '94042852'))
self.assertEqual(record.references[3].authors, "HAMANN C.;")
self.assertEqual(record.references[3].title, "")
self.assertEqual(len(record.references[3].references), 0)
#Check the two parsers agree on the essentials
self.assertEqual(seq_record.seq.tostring(), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assert_(seq_record.id in record.accessions)
#Now try using the iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(records[0], SeqRecord))
#Check matches what we got earlier without the iterator:
self.assertEqual(records[0].seq.tostring(), seq_record.seq.tostring())
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
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
self.assert_(isinstance(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', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# 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(seq_record.seq.tostring(), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assert_(seq_record.id in record.accessions)
#Now try using the iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(records[0], SeqRecord))
#Check matches what we got earlier without the iterator:
self.assertEqual(records[0].seq.tostring(), seq_record.seq.tostring())
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
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
self.assert_(isinstance(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', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# 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(seq_record.seq.tostring(), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assert_(seq_record.id in record.accessions)
#Now try using the iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(records[0], SeqRecord))
#Check matches what we got earlier without the iterator:
self.assertEqual(records[0].seq.tostring(), seq_record.seq.tostring())
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
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
self.assert_(isinstance(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', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# 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)
self.assertEqual(record.features[0], ('TRANSMEM', 8, 28, 'POTENTIAL.', ''))
self.assertEqual(record.features[1], ('TRANSMEM', 82, 102, 'POTENTIAL.', ''))
self.assertEqual(record.features[2], ('TRANSMEM', 116, 136, 'POTENTIAL.', ''))
self.assertEqual(record.features[3], ('TRANSMEM', 164, 184, 'POTENTIAL.', ''))
self.assertEqual(record.features[4], ('CONFLICT', 62, 62, 'I -> V (IN REF. 2).', ''))
self.assertEqual(record.features[5], ('CONFLICT', 135, 135, 'V -> A (IN REF. 2).', ''))
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(seq_record.seq.tostring(), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assert_(seq_record.id in record.accessions)
#Now try using the iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(records[0], SeqRecord))
#Check matches what we got earlier without the iterator:
self.assertEqual(records[0].seq.tostring(), seq_record.seq.tostring())
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
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
self.assert_(isinstance(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', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# 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)
self.assertEqual(record.features[0], ('SIGNAL', 1, 24, '', ''))
self.assertEqual(record.features[1], ('CHAIN', 25, 365, 'HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, A-2 ALPHA CHAIN.', ''))
self.assertEqual(record.features[2], ('DOMAIN', 25, 114, 'EXTRACELLULAR ALPHA-1.', ''))
self.assertEqual(record.features[3], ('DOMAIN', 115, 206, 'EXTRACELLULAR ALPHA-2.', ''))
self.assertEqual(record.features[4], ('DOMAIN', 207, 298, 'EXTRACELLULAR ALPHA-3.', ''))
self.assertEqual(record.features[5], ('DOMAIN', 299, 308, 'CONNECTING PEPTIDE.', ''))
self.assertEqual(record.features[6], ('TRANSMEM', 309, 332, '', ''))
self.assertEqual(record.features[7], ('DOMAIN', 333, 365, 'CYTOPLASMIC TAIL.', ''))
self.assertEqual(record.features[8], ('CARBOHYD', 110, 110, '', ''))
self.assertEqual(record.features[9], ('DISULFID', 125, 188, '', ''))
self.assertEqual(record.features[10], ('DISULFID', 227, 283, '', ''))
self.assertEqual(record.features[11], ('STRAND', 27, 36, '', ''))
self.assertEqual(record.features[12], ('STRAND', 45, 52, '', ''))
self.assertEqual(record.features[13], ('TURN', 53, 54, '', ''))
self.assertEqual(record.features[14], ('STRAND', 55, 61, '', ''))
self.assertEqual(record.features[15], ('TURN', 62, 63, '', ''))
self.assertEqual(record.features[16], ('STRAND', 70, 71, '', ''))
self.assertEqual(record.features[17], ('HELIX', 74, 76, '', ''))
self.assertEqual(record.features[18], ('TURN', 77, 78, '', ''))
self.assertEqual(record.features[19], ('HELIX', 81, 108, '', ''))
self.assertEqual(record.features[20], ('TURN', 109, 110, '', ''))
self.assertEqual(record.features[21], ('TURN', 113, 114, '', ''))
self.assertEqual(record.features[22], ('STRAND', 118, 127, '', ''))
self.assertEqual(record.features[23], ('TURN', 129, 130, '', ''))
self.assertEqual(record.features[24], ('STRAND', 133, 142, '', ''))
self.assertEqual(record.features[25], ('TURN', 143, 144, '', ''))
self.assertEqual(record.features[26], ('STRAND', 145, 150, '', ''))
self.assertEqual(record.features[27], ('TURN', 152, 153, '', ''))
self.assertEqual(record.features[28], ('STRAND', 157, 159, '', ''))
self.assertEqual(record.features[29], ('TURN', 163, 163, '', ''))
self.assertEqual(record.features[30], ('HELIX', 164, 173, '', ''))
self.assertEqual(record.features[31], ('TURN', 174, 175, '', ''))
self.assertEqual(record.features[32], ('HELIX', 176, 185, '', ''))
self.assertEqual(record.features[33], ('TURN', 186, 186, '', ''))
self.assertEqual(record.features[34], ('HELIX', 187, 198, '', ''))
self.assertEqual(record.features[35], ('TURN', 199, 199, '', ''))
self.assertEqual(record.features[36], ('HELIX', 200, 203, '', ''))
self.assertEqual(record.features[37], ('TURN', 204, 204, '', ''))
self.assertEqual(record.features[38], ('STRAND', 207, 207, '', ''))
self.assertEqual(record.features[39], ('STRAND', 210, 219, '', ''))
self.assertEqual(record.features[40], ('TURN', 220, 221, '', ''))
self.assertEqual(record.features[41], ('STRAND', 222, 233, '', ''))
self.assertEqual(record.features[42], ('STRAND', 238, 243, '', ''))
self.assertEqual(record.features[43], ('TURN', 244, 245, '', ''))
self.assertEqual(record.features[44], ('STRAND', 246, 247, '', ''))
self.assertEqual(record.features[45], ('HELIX', 249, 251, '', ''))
self.assertEqual(record.features[46], ('STRAND', 253, 254, '', ''))
self.assertEqual(record.features[47], ('STRAND', 258, 259, '', ''))
self.assertEqual(record.features[48], ('STRAND', 265, 274, '', ''))
self.assertEqual(record.features[49], ('TURN', 275, 276, '', ''))
self.assertEqual(record.features[50], ('HELIX', 278, 280, '', ''))
self.assertEqual(record.features[51], ('STRAND', 281, 286, '', ''))
self.assertEqual(record.features[52], ('TURN', 288, 289, '', ''))
self.assertEqual(record.features[53], ('STRAND', 294, 297, '', ''))
self.assertEqual(record.features[54], ('VARIANT', 33, 33, 'F -> Y (IN A*0205, A*0206, A*0208, A*0210 AND A*0221). /FTId=VAR_004334.', 'VAR_004334'))
self.assertEqual(record.features[55], ('VARIANT', 54, 54, 'D -> N (IN A*0221). /FTId=VAR_004335.', 'VAR_004335'))
self.assertEqual(record.features[56], ('VARIANT', 67, 67, 'Q -> R (IN A*0202, A*0205, AND A*0208). /FTId=VAR_004336.', 'VAR_004336'))
self.assertEqual(record.features[57], ('VARIANT', 90, 90, 'K -> N (IN A*0208 AND A*0220). /FTId=VAR_004337.', 'VAR_004337'))
self.assertEqual(record.features[58], ('VARIANT', 97, 98, 'TH -> ID (IN A*0211). /FTId=VAR_004338.', 'VAR_004338'))
self.assertEqual(record.features[59], ('VARIANT', 119, 119, 'V -> L (IN A*0202, A*0205, A*0208 AND A*0217). /FTId=VAR_004339.', 'VAR_004339'))
self.assertEqual(record.features[60], ('VARIANT', 121, 121, 'R -> M (IN A*0204 AND A*0217). /FTId=VAR_004340.', 'VAR_004340'))
self.assertEqual(record.features[61], ('VARIANT', 123, 123, 'Y -> C (IN A*0207 AND A*0218). /FTId=VAR_004341.', 'VAR_004341'))
self.assertEqual(record.features[62], ('VARIANT', 123, 123, 'Y -> F (IN A*0210 AND A*0217). /FTId=VAR_004342.', 'VAR_004342'))
self.assertEqual(record.features[63], ('VARIANT', 131, 131, 'W -> G (IN A*0210). /FTId=VAR_004343.', 'VAR_004343'))
self.assertEqual(record.features[64], ('VARIANT', 162, 162, 'M -> K (IN A*0218). /FTId=VAR_004344.', 'VAR_004344'))
self.assertEqual(record.features[65], ('VARIANT', 173, 173, 'A -> T (IN A*0203). /FTId=VAR_004345.', 'VAR_004345'))
self.assertEqual(record.features[66], ('VARIANT', 176, 176, 'V -> E (IN A*0203 AND A*0213). /FTId=VAR_004346.', 'VAR_004346'))
self.assertEqual(record.features[67], ('VARIANT', 180, 180, 'L -> W (IN A*0202, A*0203, A*0205 AND A*0208). /FTId=VAR_004347.', 'VAR_004347'))
self.assertEqual(record.features[68], ('VARIANT', 180, 180, 'L -> Q (IN A*0212 AND A*0213). /FTId=VAR_004348.', 'VAR_004348'))
self.assertEqual(record.features[69], ('VARIANT', 187, 187, 'T -> E (IN A*0216). /FTId=VAR_004349.', 'VAR_004349'))
self.assertEqual(record.features[70], ('VARIANT', 260, 260, 'A -> E (IN A*0209). /FTId=VAR_004350.', '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(seq_record.seq.tostring(), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assert_(seq_record.id in record.accessions)
#Now try using the iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(records[0], SeqRecord))
#Check matches what we got earlier without the iterator:
self.assertEqual(records[0].seq.tostring(), seq_record.seq.tostring())
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
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
self.assert_(isinstance(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', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# 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)
self.assertEqual(record.features[0], ('ACT_SITE', 165, 165, 'BY SIMILARITY.', ''))
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(seq_record.seq.tostring(), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assert_(seq_record.id in record.accessions)
#Now try using the iterator - note that all these
#test cases have only one record.
# With the SequenceParser
test_handle = open(datafile)
records = list(SeqIO.parse(test_handle, "swiss"))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(records[0], SeqRecord))
#Check matches what we got earlier without the iterator:
self.assertEqual(records[0].seq.tostring(), seq_record.seq.tostring())
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
test_handle = open(datafile)
records = list(SwissProt.parse(test_handle))
test_handle.close()
self.assertEqual(len(records), 1)
self.assert_(isinstance(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)
test_handle = open(datafile)
seq_record = SeqIO.read(test_handle, "swiss")
test_handle.close()
self.assert_(isinstance(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', ProteinAlphabet())")
test_handle = open(datafile)
record = SwissProt.read(test_handle)
test_handle.close()
# 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)
self.assertEqual(record.features[0], ('DOMAIN', 1, 19, 'EXTRACELLULAR (POTENTIAL).', ''))
self.assertEqual(record.features[1], ('TRANSMEM', 20, 40, '1 (POTENTIAL).', ''))
self.assertEqual(record.features[2], ('DOMAIN', 41, 58, 'CYTOPLASMIC (POTENTIAL).', ''))
self.assertEqual(record.features[3], ('TRANSMEM', 59, 79, '2 (POTENTIAL).', ''))
self.assertEqual(record.features[4], ('DOMAIN', 80, 93, 'EXTRACELLULAR (POTENTIAL).', ''))
self.assertEqual(record.features[5], ('TRANSMEM', 94, 116, '3 (POTENTIAL).', ''))
self.assertEqual(record.features[6], ('DOMAIN', 117, 137, 'CYTOPLASMIC (POTENTIAL).', ''))
self.assertEqual(record.features[7], ('TRANSMEM', 138, 158, '4 (POTENTIAL).', ''))
self.assertEqual(record.features[8], ('DOMAIN', 159, 192, 'EXTRACELLULAR (POTENTIAL).', ''))
self.assertEqual(record.features[9], ('TRANSMEM', 193, 213, '5 (POTENTIAL).', ''))
self.assertEqual(record.features[10], ('DOMAIN', 214, 260, 'CYTOPLASMIC (POTENTIAL).', ''))
self.assertEqual(record.features[11], ('TRANSMEM', 261, 281, '6 (POTENTIAL).', ''))
self.assertEqual(record.features[12], ('DOMAIN', 282, 294, 'EXTRACELLULAR (POTENTIAL).', ''))