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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 subprocess import getoutput
output = getoutput("t_coffee -version")
if "not found" not in output and "not recognized" not in output:
if "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"
# TODO: Use a temp dir for the output files:
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.aln"
self.outfile5 = "Fasta/tc_out.phy"
self.outfile6 = "Fasta/tc_out.msf"
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)
if os.path.isfile(self.outfile5):
os.remove(self.outfile5)
def test_TCoffee_fasta(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_pir(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.assertNotIn("error", 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_clustalw(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.aln "
"-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("-", "")
)
def test_TCoffee_phylip(self):
"""Round-trip through app and read PHYLIP alignment from file."""
cmdline = TCoffeeCommandline(
t_coffee_exe,
infile=self.infile1,
outfile=self.outfile5,
quiet=True,
output="phylip_aln",
)
self.assertEqual(
str(cmdline),
t_coffee_exe + " -output phylip_aln "
"-infile Fasta/fa01 -outfile Fasta/tc_out.phy -quiet",
)
stdout, stderr = cmdline()
# Can get warnings in stderr output
self.assertNotIn("error", stderr.lower(), stderr)
align = AlignIO.read(self.outfile5, "phylip")
records = list(SeqIO.parse(self.infile1, "fasta"))
self.assertEqual(len(records), len(align))
for old, new in zip(records, align):
# TCoffee does strict 10 character truncation as per original PHYLIP
self.assertEqual(old.id[:10], new.id[:10])
self.assertEqual(
str(new.seq).replace("-", ""), str(old.seq).replace("-", "")
)
def test_TCoffee_msf(self):
"""Round-trip through app and read GCG MSF alignment from file."""
cmdline = TCoffeeCommandline(
t_coffee_exe,
infile=self.infile1,
outfile=self.outfile6,
quiet=True,
output="msf_aln",
)
self.assertEqual(
str(cmdline),
t_coffee_exe
+ " -output msf_aln -infile Fasta/fa01 -outfile Fasta/tc_out.msf -quiet",
)
stdout, stderr = cmdline()
# Can get warnings in stderr output
self.assertNotIn("error", stderr.lower(), stderr)
align = AlignIO.read(self.outfile6, "msf")
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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