# Copyright 2008-2011 by Peter Cock. All rights reserved. # Revisions copyright 2012 by Christian Brueffer. 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. """Tests for ClustalOmega tool.""" import sys import os import unittest from subprocess import getoutput from Bio import MissingExternalDependencyError from Bio import SeqIO from Bio import AlignIO from Bio.Align.Applications import ClustalOmegaCommandline from Bio.Application import ApplicationError ################################################################# # Try to avoid problems when the OS is in another language os.environ["LANG"] = "C" clustalo_exe = None try: output = getoutput("clustalo --help") if output.startswith("Clustal Omega"): clustalo_exe = "clustalo" except FileNotFoundError: pass if not clustalo_exe: raise MissingExternalDependencyError( "Install clustalo if you want to use Clustal Omega from Biopython." ) class ClustalOmegaTestCase(unittest.TestCase): def setUp(self): self.files_to_clean = set() def tearDown(self): for filename in self.files_to_clean: if os.path.isfile(filename): os.remove(filename) def standard_test_procedure(self, cline): """Shared test procedure used by all tests.""" # Overwrite existing files. cline.force = True # Mark output files for later cleanup. self.add_file_to_clean(cline.outfile) if cline.guidetree_out: self.add_file_to_clean(cline.guidetree_out) input_records = SeqIO.to_dict(SeqIO.parse(cline.infile, "fasta")) self.assertEqual(str(eval(repr(cline))), str(cline)) output, error = cline() self.assertTrue(not output or output.strip().startswith("CLUSTAL")) # Test if ClustalOmega executed successfully. self.assertTrue( error.strip() == "" or error.startswith("WARNING: Sequence type is DNA.") or error.startswith("WARNING: DNA alignment is still experimental.") ) # Check the output... align = AlignIO.read(cline.outfile, "clustal") output_records = SeqIO.to_dict(SeqIO.parse(cline.outfile, "clustal")) self.assertEqual( len(set(input_records.keys())), len(set(output_records.keys())) ) for record in align: self.assertEqual(str(record.seq), str(output_records[record.id].seq)) # TODO - Try and parse this with Bio.Nexus? if cline.guidetree_out: self.assertTrue(os.path.isfile(cline.guidetree_out)) def add_file_to_clean(self, filename): """Add a file for deferred removal by the tearDown routine.""" self.files_to_clean.add(filename) ################################################################# class ClustalOmegaTestErrorConditions(ClustalOmegaTestCase): def test_empty_file(self): """Test an empty file.""" input_file = "does_not_exist.fasta" self.assertFalse(os.path.isfile(input_file)) cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file) try: stdout, stderr = cline() except ApplicationError as err: self.assertTrue( "Cannot open sequence file" in str(err) or "Cannot open input file" in str(err) or "Non-zero return code" in str(err), str(err), ) else: self.fail("Should have failed, returned:\n%s\n%s" % (stdout, stderr)) def test_single_sequence(self): """Test an input file containing a single sequence.""" input_file = "Fasta/f001" self.assertTrue(os.path.isfile(input_file)) self.assertEqual(len(list(SeqIO.parse(input_file, "fasta"))), 1) cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file) try: stdout, stderr = cline() except ApplicationError as err: self.assertIn("contains 1 sequence, nothing to align", str(err)) else: self.fail("Should have failed, returned:\n%s\n%s" % (stdout, stderr)) def test_invalid_format(self): """Test an input file in an invalid format.""" input_file = "Medline/pubmed_result1.txt" self.assertTrue(os.path.isfile(input_file)) cline = ClustalOmegaCommandline(clustalo_exe, infile=input_file) try: stdout, stderr = cline() except ApplicationError as err: # Ideally we'd catch the return code and raise the specific # error for "invalid format". self.assertIn("Can't determine format of sequence file", str(err)) else: self.fail("Should have failed, returned:\n%s\n%s" % (stdout, stderr)) ################################################################# class ClustalOmegaTestNormalConditions(ClustalOmegaTestCase): def test_simple_fasta(self): """Test a simple fasta file.""" input_file = "Registry/seqs.fasta" output_file = "temp_test.aln" cline = ClustalOmegaCommandline( clustalo_exe, infile=input_file, outfile=output_file, outfmt="clustal" ) self.standard_test_procedure(cline) def test_properties(self): """Test setting options via properties.""" input_file = "Registry/seqs.fasta" output_file = "temp_test.aln" cline = ClustalOmegaCommandline(clustalo_exe) cline.infile = input_file cline.outfile = output_file cline.outfmt = "clustal" self.standard_test_procedure(cline) def test_input_filename_with_space(self): """Test an input filename containing a space.""" input_file = "Clustalw/temp horses.fasta" with open(input_file, "w") as handle: SeqIO.write(SeqIO.parse("Phylip/hennigian.phy", "phylip"), handle, "fasta") output_file = "temp_test.aln" cline = ClustalOmegaCommandline( clustalo_exe, infile=input_file, outfile=output_file, outfmt="clustal" ) self.add_file_to_clean(input_file) self.standard_test_procedure(cline) def test_output_filename_with_spaces(self): """Test an output filename containing spaces.""" input_file = "Registry/seqs.fasta" output_file = "temp with spaces.aln" cline = ClustalOmegaCommandline( clustalo_exe, infile=input_file, outfile=output_file, outfmt="clustal" ) self.standard_test_procedure(cline) def test_large_fasta_file(self): """Test a large fasta input file.""" # Create a large input file by converting another example file # (See Bug 2804, this will produce so much output on stdout that # subprocess could suffer a deadlock and hang). Using all the # records should show the deadlock but is very slow - just thirty # seems to lockup on Mac OS X, even 20 on Linux (without the fix). input_file = "temp_cw_prot.fasta" records = list(SeqIO.parse("NBRF/Cw_prot.pir", "pir"))[:40] with open(input_file, "w") as handle: SeqIO.write(records, handle, "fasta") del handle, records output_file = "temp_cw_prot.aln" cline = ClustalOmegaCommandline( clustalo_exe, infile=input_file, outfile=output_file, outfmt="clustal" ) self.add_file_to_clean(input_file) self.standard_test_procedure(cline) def test_newtree_files(self): """Test requesting a guide tree.""" input_file = "Fasta/f002" output_file = "temp_test.aln" newtree_file = "temp_test.dnd" cline = ClustalOmegaCommandline( clustalo_exe, infile=input_file, outfile=output_file, guidetree_out=newtree_file, outfmt="clustal", ) self.standard_test_procedure(cline) cline.guidetree_out = "temp with space.dnd" self.standard_test_procedure(cline) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)