# 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)