# 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 os import sys import unittest import warnings from Bio import AlignIO from Bio import BiopythonDeprecationWarning from Bio import MissingExternalDependencyError from Bio import SeqIO with warnings.catch_warnings(): warnings.simplefilter("ignore", category=BiopythonDeprecationWarning) 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)