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# Copyright 2012 by Christian Brueffer. 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.
import glob
import os
import shutil
import sys
import unittest
from Bio import MissingExternalDependencyError
from Bio import SeqIO
from Bio.Application import ApplicationError
from Bio.motifs.applications import XXmotifCommandline
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
xxmotif_exe = None
if sys.platform == "win32":
# TODO
raise MissingExternalDependencyError("Testing this on Windows is not implemented yet")
else:
from Bio._py3k import getoutput
output = getoutput("XXmotif")
if output.find("== XXmotif version") != -1:
xxmotif_exe = "XXmotif"
if not xxmotif_exe:
raise MissingExternalDependencyError(
"Install XXmotif if you want to use XXmotif from Biopython.")
class XXmotifTestCase(unittest.TestCase):
def setUp(self):
self.out_dir = "xxmotif-temp"
self.files_to_clean = set()
def tearDown(self):
for filename in self.files_to_clean:
if os.path.isfile(filename):
os.remove(filename)
if os.path.isdir(self.out_dir):
shutil.rmtree(self.out_dir)
def standard_test_procedure(self, cline):
"""Standard testing procedure used by all tests."""
output, error = cline()
self.assertTrue(os.path.isdir(self.out_dir))
self.assertTrue(glob.glob(os.path.join(self.out_dir, "*.meme")))
self.assertTrue(glob.glob(os.path.join(self.out_dir, "*_MotifFile.txt")))
self.assertTrue(glob.glob(os.path.join(self.out_dir, "*_Pvals.txt")))
self.assertTrue(glob.glob(os.path.join(self.out_dir, "*.pwm")))
self.assertTrue(glob.glob(os.path.join(self.out_dir, "*_sequence.txt")))
# TODO
# Parsing the MEME file would be nice, but unfortunately the
# MEME parser does not like what XXmotif produces yet.
def copy_and_mark_for_cleanup(self, path):
"""
XXmotif currently only handles a canonical filename as input, no paths.
This method copies the specified file in the specified path to the
current working directory and marks it for removal.
"""
filename = os.path.split(path)[1]
shutil.copyfile(path, filename)
self.add_file_to_clean(filename)
return filename
def add_file_to_clean(self, filename):
"""Adds a file for deferred removal by the tearDown routine."""
self.files_to_clean.add(filename)
class XXmotifTestErrorConditions(XXmotifTestCase):
def test_empty_file(self):
"""Test a non-existing input file."""
input_file = "does_not_exist.fasta"
self.assertFalse(os.path.isfile(input_file))
cline = XXmotifCommandline(outdir=self.out_dir,
seqfile=input_file)
try:
stdout, stderr = cline()
except ApplicationError as err:
self.assertEqual(err.returncode, 255)
else:
self.fail("Should have failed, returned:\n%s\n%s" % (stdout, stderr))
def test_invalid_format(self):
"""Test an input file in an invalid format."""
input_file = self.copy_and_mark_for_cleanup("Medline/pubmed_result1.txt")
cline = XXmotifCommandline(outdir=self.out_dir,
seqfile=input_file)
try:
stdout, stderr = cline()
except ApplicationError as err:
self.assertEqual(err.returncode, 255)
else:
self.fail("Should have failed, returned:\n%s\n%s" % (stdout, stderr))
def test_output_directory_with_space(self):
"""Test an output directory containing a space."""
temp_out_dir = "xxmotif test"
input_file = self.copy_and_mark_for_cleanup("Fasta/f002")
try:
cline = XXmotifCommandline(outdir=temp_out_dir,
seqfile=input_file)
except ValueError:
pass
else:
self.fail("expected ValueError")
class XXmotifTestNormalConditions(XXmotifTestCase):
def test_fasta_one_sequence(self):
"""Test a fasta input file containing only one sequence."""
input_file = "seq.fasta"
handle = open(input_file, "w")
record = list(SeqIO.parse("Registry/seqs.fasta", "fasta"))[0]
SeqIO.write(record, handle, "fasta")
handle.close()
del handle, record
cline = XXmotifCommandline(outdir=self.out_dir,
seqfile=input_file)
self.add_file_to_clean(input_file)
self.standard_test_procedure(cline)
def test_properties(self):
"""Test setting options via properties."""
input_file = self.copy_and_mark_for_cleanup("Fasta/f002")
cline = XXmotifCommandline(outdir=self.out_dir,
seqfile=input_file)
cline.revcomp = True
cline.pseudo = 20
cline.startmotif = "ACGGGT"
self.standard_test_procedure(cline)
def test_large_fasta_file(self):
"""Test a large fasta input file."""
input_file = "temp_b_nuc.fasta"
handle = open(input_file, "w")
records = list(SeqIO.parse("NBRF/B_nuc.pir", "pir"))
SeqIO.write(records, handle, "fasta")
handle.close()
del handle, records
cline = XXmotifCommandline(outdir=self.out_dir,
seqfile=input_file)
self.add_file_to_clean(input_file)
self.standard_test_procedure(cline)
def test_input_filename_with_space(self):
"""Test an input filename containing a space."""
input_file = "temp horses.fasta"
handle = open(input_file, "w")
SeqIO.write(SeqIO.parse("Phylip/hennigian.phy", "phylip"), handle, "fasta")
handle.close()
cline = XXmotifCommandline(outdir=self.out_dir,
seqfile=input_file)
self.add_file_to_clean(input_file)
self.standard_test_procedure(cline)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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