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# Copyright 2009 by Cymon J. Cox. All rights reserved.
# Revisions 2009 copyright 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.
"""Unittests for Bio.Align.Applications interface for DIALIGN2-2."""
import sys
import os
import unittest
from Bio import MissingExternalDependencyError
from Bio.Align.Applications import DialignCommandline
# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
dialign_exe = None
if sys.platform == "win32":
raise MissingExternalDependencyError("DIALIGN2-2 not available on Windows")
else:
from Bio._py3k import getoutput
output = getoutput("dialign2-2")
if "not found" not in output and "dialign2-2" in output.lower():
dialign_exe = "dialign2-2"
if "DIALIGN2_DIR" not in os.environ:
raise MissingExternalDependencyError(
"Environment variable DIALIGN2_DIR for DIALIGN2-2 missing.")
if not os.path.isdir(os.environ["DIALIGN2_DIR"]):
raise MissingExternalDependencyError(
"Environment variable DIALIGN2_DIR for DIALIGN2-2 is not a valid directory.")
if not os.path.isfile(os.path.join(os.environ["DIALIGN2_DIR"], "BLOSUM")):
raise MissingExternalDependencyError(
"Environment variable DIALIGN2_DIR directory missing BLOSUM file.")
# TODO - check for tp400_dna, tp400_prot and tp400_trans too?
if not dialign_exe:
raise MissingExternalDependencyError(
"Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper.")
class DialignApplication(unittest.TestCase):
def setUp(self):
self.infile1 = "Fasta/f002"
# Standard output file
self.outfile1 = "Fasta/f002.ali"
# MSF output
self.outfile2 = "Fasta/f002.ms"
def tearDown(self):
if os.path.isfile(self.outfile1):
os.remove(self.outfile1)
if os.path.isfile(self.outfile2):
os.remove(self.outfile2)
def test_Dialign_simple(self):
"""Simple round-trip through app with infile.
"""
# Test using keyword arguments:
cmdline = DialignCommandline(dialign_exe, input=self.infile1)
self.assertEqual(str(cmdline), dialign_exe + " Fasta/f002")
stdout, stderr = cmdline()
self.assertEqual(stderr, "")
self.assertEqual(stdout, "")
self.assertTrue(os.path.exists(self.outfile1))
def test_Dialign_simple_with_options(self):
"""Simple round-trip through app with infile and options
"""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-max_link", True)
cmdline.set_parameter("stars", 4)
self.assertEqual(str(cmdline), dialign_exe +
" -max_link -stars 4 Fasta/f002")
stdout, stderr = cmdline()
self.assertEqual(stderr, "")
self.assertEqual(stdout, "")
self.assertTrue(os.path.exists(self.outfile1))
def test_Dialign_simple_with_MSF_output(self):
"""Simple round-trip through app with infile, output MSF
"""
cmdline = DialignCommandline(dialign_exe)
# Test with properties
cmdline.input = self.infile1
cmdline.msf = True
self.assertEqual(str(cmdline), dialign_exe + " -msf Fasta/f002")
stdout, stderr = cmdline()
self.assertEqual(stderr, "")
self.assertEqual(stdout, "")
self.assertTrue(os.path.exists(self.outfile1))
self.assertTrue(os.path.exists(self.outfile2))
def test_Dialign_complex_command_line(self):
"""Round-trip through app with complex command line."""
cmdline = DialignCommandline(dialign_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("-nt", True)
cmdline.set_parameter("-thr", 4)
cmdline.set_parameter("stars", 9)
cmdline.set_parameter("-ow", True)
cmdline.set_parameter("mask", True)
cmdline.set_parameter("-cs", True)
self.assertEqual(str(cmdline), dialign_exe +
" -cs -mask -nt -ow -stars 9 -thr 4 Fasta/f002")
stdout, stderr = cmdline()
self.assertEqual(stderr, "")
self.assertTrue(os.path.exists(self.outfile1))
self.assertTrue(stdout.startswith(" e_len = 633"))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)