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# 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
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:
from Bio._py3k import getoutput
output = 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.")
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)
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(self.outfile1, "clustal")
records = list(SeqIO.parse(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("-", ""))
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(self.outfile3, "pir")
records = list(SeqIO.parse(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("-", ""))
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(self.outfile4, "clustal")
records = list(SeqIO.parse(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)
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