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# Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO writing."""
import os
import unittest
from Bio import BiopythonExperimentalWarning
import warnings
with warnings.catch_warnings():
warnings.simplefilter('ignore', BiopythonExperimentalWarning)
from Bio import SearchIO
from search_tests_common import compare_search_obj
class WriteCases(unittest.TestCase):
def tearDown(self):
if os.path.exists(self.out):
os.remove(self.out)
def parse_write_and_compare(self, source_file, source_format, out_file,
out_format, **kwargs):
"""Compares parsed QueryResults after they have been written to a file."""
source_qresults = list(SearchIO.parse(source_file, source_format,
**kwargs))
SearchIO.write(source_qresults, out_file, out_format, **kwargs)
out_qresults = list(SearchIO.parse(out_file, out_format, **kwargs))
for source, out in zip(source_qresults, out_qresults):
self.assertTrue(compare_search_obj(source, out))
def read_write_and_compare(self, source_file, source_format, out_file,
out_format, **kwargs):
"""Compares read QueryResults after it has been written to a file."""
source_qresult = SearchIO.read(source_file, source_format, **kwargs)
SearchIO.write(source_qresult, out_file, out_format, **kwargs)
out_qresult = SearchIO.read(out_file, out_format, **kwargs)
self.assertTrue(compare_search_obj(source_qresult, out_qresult))
class BlastXmlWriteCases(WriteCases):
fmt = 'blast-xml'
out = os.path.join('Blast', 'test_write.xml')
def test_write_single_from_blastxml(self):
"""Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml)"""
source = os.path.join('Blast', 'xml_2226_blastp_004.xml')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
self.read_write_and_compare(source, self.fmt, self.out, self.fmt)
def test_write_multiple_from_blastxml(self):
"""Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml)"""
source = os.path.join('Blast', 'xml_2226_blastp_001.xml')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
class BlastTabWriteCases(WriteCases):
fmt = 'blast-tab'
out = os.path.join('Blast', 'test_write.txt')
def test_write_single_from_blasttab(self):
"""Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt)"""
source = os.path.join('Blast', 'tab_2226_tblastn_004.txt')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
self.read_write_and_compare(source, self.fmt, self.out, self.fmt)
def test_write_multiple_from_blasttab(self):
"""Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt)"""
source = os.path.join('Blast', 'tab_2226_tblastn_001.txt')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
def test_write_single_from_blasttabc(self):
"""Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt)"""
source = os.path.join('Blast', 'tab_2226_tblastn_008.txt')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt, comments=True)
self.read_write_and_compare(source, self.fmt, self.out, self.fmt, comments=True)
def test_write_multiple_from_blasttabc(self):
"""Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt)"""
source = os.path.join('Blast', 'tab_2226_tblastn_005.txt')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt, comments=True)
def test_write_multiple_from_blasttabc_allfields(self):
"""Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt)"""
source = os.path.join('Blast', 'tab_2228_tblastx_001.txt')
fields = ['qseqid', 'qgi', 'qacc', 'qaccver', 'qlen', 'sseqid',
'sallseqid', 'sgi', 'sallgi', 'sacc', 'saccver', 'sallacc',
'slen', 'qstart', 'qend', 'sstart', 'send', 'qseq', 'sseq',
'evalue', 'bitscore', 'score', 'length', 'pident', 'nident',
'mismatch', 'positive', 'gapopen', 'gaps', 'ppos', 'frames',
'qframe', 'sframe', 'btop', 'staxids', 'sscinames', 'scomnames',
'sblastnames', 'sskingdoms', 'stitle', 'salltitles', 'sstrand',
'qcovs', 'qcovhsp']
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt, comments=True, fields=fields)
class HmmerTabWriteCases(WriteCases):
fmt = 'hmmer3-tab'
out = os.path.join('Hmmer', 'test_write.txt')
def test_write_single_from_hmmertab(self):
"""Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out)"""
source = os.path.join('Hmmer', 'tab_30_hmmscan_004.out')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
self.read_write_and_compare(source, self.fmt, self.out, self.fmt)
def test_write_multiple_from_hmmertab(self):
"""Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out)"""
source = os.path.join('Hmmer', 'tab_30_hmmscan_001.out')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
class HmmerDomtabWriteCases(WriteCases):
out = os.path.join('Hmmer', 'test_write.txt')
def test_write_single_from_hmmscandomtab(self):
"""Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out)"""
source = os.path.join('Hmmer', 'domtab_30_hmmscan_004.out')
fmt = 'hmmscan3-domtab'
self.parse_write_and_compare(source, fmt, self.out, fmt)
self.read_write_and_compare(source, fmt, self.out, fmt)
def test_write_multiple_from_hmmscandomtab(self):
"""Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out)"""
source = os.path.join('Hmmer', 'domtab_30_hmmscan_001.out')
fmt = 'hmmscan3-domtab'
self.parse_write_and_compare(source, fmt, self.out, fmt)
def test_write_single_from_hmmsearchdomtab(self):
"""Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out)"""
source = os.path.join('Hmmer', 'domtab_30_hmmsearch_001.out')
fmt = 'hmmsearch3-domtab'
self.parse_write_and_compare(source, fmt, self.out, fmt)
self.read_write_and_compare(source, fmt, self.out, fmt)
class BlatPslWriteCases(WriteCases):
fmt = 'blat-psl'
out = os.path.join('Blat', 'test_write.txt')
def test_write_single_from_blatpsl(self):
"""Test blat-psl writing from blat-psl, single query (psl_34_004.psl)"""
source = os.path.join('Blat', 'psl_34_004.psl')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
self.read_write_and_compare(source, self.fmt, self.out, self.fmt)
def test_write_multiple_from_blatpsl(self):
"""Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl)"""
source = os.path.join('Blat', 'psl_34_001.psl')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt)
def test_write_single_from_blatpslx(self):
"""Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx)"""
source = os.path.join('Blat', 'pslx_34_004.pslx')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt, pslx=True)
self.read_write_and_compare(source, self.fmt, self.out, self.fmt, pslx=True)
def test_write_multiple_from_blatpslx(self):
"""Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx)"""
source = os.path.join('Blat', 'pslx_34_001.pslx')
self.parse_write_and_compare(source, self.fmt, self.out, self.fmt, pslx=True)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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