Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

159 lines (117 sloc) 7.326 kb
# 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 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)
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)
Jump to Line
Something went wrong with that request. Please try again.