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test_SwissProt.py
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test_SwissProt.py
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#!/usr/bin/env python
# Copyright 2009 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2010 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 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.assertTrue(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(str(seq_record.seq), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assertTrue(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.assertTrue(isinstance(records[0], SeqRecord))
# Check matches what we got earlier without the iterator:
self.assertEqual(str(records[0].seq), str(seq_record.seq))
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.assertTrue(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.assertTrue(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(str(seq_record.seq), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assertTrue(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.assertTrue(isinstance(records[0], SeqRecord))
# Check matches what we got earlier without the iterator:
self.assertEqual(str(records[0].seq), str(seq_record.seq))
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.assertTrue(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.assertTrue(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(str(seq_record.seq), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assertTrue(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.assertTrue(isinstance(records[0], SeqRecord))
# Check matches what we got earlier without the iterator:
self.assertEqual(str(records[0].seq), str(seq_record.seq))
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.assertTrue(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.assertTrue(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(str(seq_record.seq), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assertTrue(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.assertTrue(isinstance(records[0], SeqRecord))
# Check matches what we got earlier without the iterator:
self.assertEqual(str(records[0].seq), str(seq_record.seq))
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.assertTrue(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.assertTrue(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(str(seq_record.seq), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assertTrue(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.assertTrue(isinstance(records[0], SeqRecord))
# Check matches what we got earlier without the iterator:
self.assertEqual(str(records[0].seq), str(seq_record.seq))
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.assertTrue(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.assertTrue(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(str(seq_record.seq), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assertTrue(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.assertTrue(isinstance(records[0], SeqRecord))
# Check matches what we got earlier without the iterator:
self.assertEqual(str(records[0].seq), str(seq_record.seq))
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.assertTrue(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.assertTrue(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(str(seq_record.seq), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assertTrue(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.assertTrue(isinstance(records[0], SeqRecord))
# Check matches what we got earlier without the iterator:
self.assertEqual(str(records[0].seq), str(seq_record.seq))
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.assertTrue(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.assertTrue(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).', 'VAR_004334'))
self.assertEqual(record.features[55], ('VARIANT', 54, 54, 'D -> N (IN A*0221).', 'VAR_004335'))
self.assertEqual(record.features[56], ('VARIANT', 67, 67, 'Q -> R (IN A*0202, A*0205, AND A*0208).', 'VAR_004336'))
self.assertEqual(record.features[57], ('VARIANT', 90, 90, 'K -> N (IN A*0208 AND A*0220).', 'VAR_004337'))
self.assertEqual(record.features[58], ('VARIANT', 97, 98, 'TH -> ID (IN A*0211).', 'VAR_004338'))
self.assertEqual(record.features[59], ('VARIANT', 119, 119, 'V -> L (IN A*0202, A*0205, A*0208 AND A*0217).', 'VAR_004339'))
self.assertEqual(record.features[60], ('VARIANT', 121, 121, 'R -> M (IN A*0204 AND A*0217).', 'VAR_004340'))
self.assertEqual(record.features[61], ('VARIANT', 123, 123, 'Y -> C (IN A*0207 AND A*0218).', 'VAR_004341'))
self.assertEqual(record.features[62], ('VARIANT', 123, 123, 'Y -> F (IN A*0210 AND A*0217).', 'VAR_004342'))
self.assertEqual(record.features[63], ('VARIANT', 131, 131, 'W -> G (IN A*0210).', 'VAR_004343'))
self.assertEqual(record.features[64], ('VARIANT', 162, 162, 'M -> K (IN A*0218).', 'VAR_004344'))
self.assertEqual(record.features[65], ('VARIANT', 173, 173, 'A -> T (IN A*0203).', 'VAR_004345'))
self.assertEqual(record.features[66], ('VARIANT', 176, 176, 'V -> E (IN A*0203 AND A*0213).', 'VAR_004346'))
self.assertEqual(record.features[67], ('VARIANT', 180, 180, 'L -> W (IN A*0202, A*0203, A*0205 AND A*0208).', 'VAR_004347'))
self.assertEqual(record.features[68], ('VARIANT', 180, 180, 'L -> Q (IN A*0212 AND A*0213).', 'VAR_004348'))
self.assertEqual(record.features[69], ('VARIANT', 187, 187, 'T -> E (IN A*0216).', 'VAR_004349'))
self.assertEqual(record.features[70], ('VARIANT', 260, 260, 'A -> E (IN A*0209).', '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(str(seq_record.seq), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assertTrue(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.assertTrue(isinstance(records[0], SeqRecord))
# Check matches what we got earlier without the iterator:
self.assertEqual(str(records[0].seq), str(seq_record.seq))
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.assertTrue(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.assertTrue(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(str(seq_record.seq), record.sequence)
self.assertEqual(seq_record.description, record.description)
self.assertEqual(seq_record.name, record.entry_name)
self.assertTrue(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.assertTrue(isinstance(records[0], SeqRecord))
# Check matches what we got earlier without the iterator:
self.assertEqual(str(records[0].seq), str(seq_record.seq))
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.assertTrue(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.assertTrue(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).', ''))
self.assertEqual(record.features[13], ('TRANSMEM', 295, 315, '7 (POTENTIAL).', ''))
self.assertEqual(record.features[14], ('DOMAIN', 316, 388, 'CYTOPLASMIC (POTENTIAL).', ''))