Logo Search packages:      
Sourcecode: python-biopython version File versions  Download package

test_TCoffee_tool.py

# Copyright 2009 by Cymon J. Cox.  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 TCOFFEE."""

import sys
import os
import unittest
import subprocess
from cStringIO import StringIO
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import TCoffeeCommandline

#Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'

t_coffee_exe = None
if sys.platform=="win32":
    raise MissingExternalDependencyError(\
        "Testing TCOFFEE on Windows not supported yet")
else:
    import commands
    output = commands.getoutput("t_coffee -version")
    if "not found" not in output \
    and ("t_coffee" in output.lower() or "t-coffee" in output.lower()):
        t_coffee_exe = "t_coffee"

if not t_coffee_exe:
    raise MissingExternalDependencyError(\
        "Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.")

00033 class TCoffeeApplication(unittest.TestCase):

    def setUp(self):
        self.infile1 = "Fasta/fa01"
        self.outfile1 = "fa01.aln"
        self.outfile2 = "fa01.html" #Written by default when no output set
        self.outfile3 = "Fasta/tc_out.pir"
        self.outfile4 = "Fasta/tc_out.phy"

    def tearDown(self):
        if os.path.isfile(self.outfile1):
            os.remove(self.outfile1)
        if os.path.isfile(self.outfile2):
            os.remove(self.outfile2)
        if os.path.isfile(self.outfile3):
            os.remove(self.outfile3)
        if os.path.isfile(self.outfile4):
            os.remove(self.outfile4)

00052     def test_TCoffee_1(self):
        """Round-trip through app and read clustal alignment from file
        """
        cmdline = TCoffeeCommandline(t_coffee_exe, infile=self.infile1)
        self.assertEqual(str(cmdline), t_coffee_exe + " -infile Fasta/fa01")
        stdout, stderr = cmdline()
        self.assertTrue(stderr.strip().startswith("PROGRAM: T-COFFEE"))
        align = AlignIO.read(open(self.outfile1), "clustal")
        records = list(SeqIO.parse(open(self.infile1),"fasta"))
        self.assertEqual(len(records),len(align))
        for old, new in zip(records, align):
            self.assertEqual(old.id, new.id)
            self.assertEqual(str(new.seq).replace("-",""), str(old.seq).replace("-",""))

00066     def test_TCoffee_2(self):
        """Round-trip through app and read pir alignment from file
        """
        cmdline = TCoffeeCommandline(t_coffee_exe, quiet=True)
        cmdline.infile = self.infile1
        cmdline.outfile = self.outfile3
        cmdline.output = "pir_aln"
        self.assertEqual(str(cmdline), t_coffee_exe + " -output pir_aln "
                    "-infile Fasta/fa01 -outfile Fasta/tc_out.pir -quiet")
        stdout, stderr = cmdline()
        #Can get warnings in stderr output
        self.assertTrue("error" not in stderr.lower(), stderr)
        align = AlignIO.read(open(self.outfile3), "pir")
        records = list(SeqIO.parse(open(self.infile1),"fasta"))
        self.assertEqual(len(records),len(align))
        for old, new in zip(records, align):
            self.assertEqual(old.id, new.id)
            self.assertEqual(str(new.seq).replace("-",""), str(old.seq).replace("-",""))

00085     def test_TCoffee_3(self):
        """Round-trip through app and read clustalw alignment from file
        """
        cmdline = TCoffeeCommandline(t_coffee_exe, gapopen=-2)
        cmdline.infile = self.infile1
        cmdline.outfile = self.outfile4
        cmdline.set_parameter("output", "clustalw_aln")
        cmdline.outorder = "input"
        cmdline.set_parameter("gapext", -5)
        cmdline.type = "protein"
        self.assertEqual(str(cmdline), t_coffee_exe + " -output clustalw_aln "
                         "-infile Fasta/fa01 -outfile Fasta/tc_out.phy "
                         "-type protein -outorder input -gapopen -2 -gapext -5")
        stdout, stderr = cmdline()
        self.assertTrue(stderr.strip().startswith("PROGRAM: T-COFFEE"))
        align = AlignIO.read(open(self.outfile4), "clustal")
        records = list(SeqIO.parse(open(self.infile1),"fasta"))
        self.assertEqual(len(records),len(align))
        for old, new in zip(records, align):
            self.assertEqual(old.id, new.id)
            self.assertEqual(str(new.seq).replace("-",""), str(old.seq).replace("-",""))

if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity = 2)
    unittest.main(testRunner=runner)

Generated by  Doxygen 1.6.0   Back to index