# 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 PRANK.""" import sys import os import unittest from Bio.Application import _escape_filename from Bio import AlignIO from Bio import SeqIO from Bio import MissingExternalDependencyError from Bio.Align.Applications import PrankCommandline from Bio.Nexus.Nexus import NexusError # Try to avoid problems when the OS is in another language os.environ["LANG"] = "C" prank_exe = None if sys.platform == "win32": try: # This can vary depending on the Windows language. prog_files = os.environ["PROGRAMFILES"] except KeyError: prog_files = r"C:\Program Files" # For Windows, PRANK just comes as a zip file which contains the # prank.exe file which the user could put anywhere. We'll try a few # sensible locations under Program Files... and then the full path. likely_dirs = [ "", # Current dir prog_files, os.path.join(prog_files, "Prank"), ] + sys.path for folder in likely_dirs: if os.path.isdir(folder): if os.path.isfile(os.path.join(folder, "prank.exe")): prank_exe = os.path.join(folder, "prank.exe") break if prank_exe: break else: from subprocess import getoutput output = getoutput("prank") if "not found" not in output and "not recognized" not in output: if "prank" in output.lower(): prank_exe = "prank" if not prank_exe: raise MissingExternalDependencyError( "Install PRANK if you want to use the Bio.Align.Applications wrapper." ) class PrankApplication(unittest.TestCase): def setUp(self): self.infile1 = "Fasta/fa01" def tearDown(self): """Remove generated files. output.1.dnd output.1.fas output.1.xml output.2.dnd output.2.fas output.2.xml """ if os.path.isfile("output.1.dnd"): os.remove("output.1.dnd") if os.path.isfile("output.1.fas"): os.remove("output.1.fas") if os.path.isfile("output.1.xml"): os.remove("output.1.xml") if os.path.isfile("output.2.dnd"): os.remove("output.2.dnd") if os.path.isfile("output.2.fas"): os.remove("output.2.fas") if os.path.isfile("output.2.xml"): os.remove("output.2.xml") if os.path.isfile("output.1.nex"): os.remove("output.1.nex") if os.path.isfile("output.2.nex"): os.remove("output.2.nex") def test_Prank_simple(self): """Simple round-trip through app with infile. output.?.??? files written to cwd - no way to redirect """ cmdline = PrankCommandline(prank_exe) cmdline.set_parameter("d", self.infile1) self.assertEqual(str(cmdline), _escape_filename(prank_exe) + " -d=Fasta/fa01") self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) output, error = cmdline() self.assertEqual(error, "") self.assertIn("Total time", output) def test_Prank_simple_with_NEXUS_output(self): """Simple round-trip through app with infile, output in NEXUS. output.?.??? files written to cwd - no way to redirect """ records = list(SeqIO.parse(self.infile1, "fasta")) # Try using keyword argument, cmdline = PrankCommandline(prank_exe, d=self.infile1) # Try using a property, cmdline.d = self.infile1 cmdline.f = 17 # NEXUS format cmdline.set_parameter("dots", True) self.assertEqual( str(cmdline), _escape_filename(prank_exe) + " -d=Fasta/fa01 -f=17 -dots" ) self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) stdout, stderr = cmdline() self.assertIn("Total time", stdout) self.assertEqual(stderr, "") try: if os.path.isfile("output.best.nex"): # Prank v.130820 and perhaps earlier use ".best.*" output names nex_fname = "output.best.nex" elif os.path.isfile("output.2.nex"): # Older Prank versions use ".2.*" output names nex_fname = "output.2.nex" else: raise RuntimeError("Can't find PRANK's NEXUS output (*.nex)") align = AlignIO.read(nex_fname, "nexus") for old, new in zip(records, align): # Old versions of Prank reduced name to 9 chars self.assertTrue(old.id == new.id or old.id[:9] == new.id) # infile1 has alignment gaps in it self.assertEqual( str(new.seq).replace("-", ""), str(old.seq).replace("-", "") ) except NexusError: # See bug 3119, # Bio.Nexus can't parse output from prank v100701 (1 July 2010) pass def test_Prank_complex_command_line(self): """Round-trip with complex command line.""" cmdline = PrankCommandline(prank_exe) cmdline.set_parameter("d", self.infile1) cmdline.set_parameter("-gaprate", 0.321) cmdline.set_parameter("gapext", 0.6) cmdline.set_parameter("-dots", 1) # i.e. True # Try using a property: cmdline.kappa = 3 cmdline.skipins = True cmdline.set_parameter("-once", True) cmdline.realbranches = True self.assertEqual( str(cmdline), _escape_filename(prank_exe) + " -d=Fasta/fa01" + " -dots -gaprate=0.321 -gapext=0.6 -kappa=3" + " -once -skipins -realbranches", ) self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) stdout, stderr = cmdline() self.assertIn("Total time", stdout) class PrankConversion(unittest.TestCase): def setUp(self): # As these reads are all 36, it can be seen as pre-aligned: self.input = "Quality/example.fasta" self.output = "temp with space" # prefix, PRANK will pick extensions def conversion(self, prank_number, prank_ext, format): """Get PRANK to do a conversion, and check it with SeqIO.""" filename = "%s.%s" % (self.output, prank_ext) if os.path.isfile(filename): os.remove(filename) cmdline = PrankCommandline( prank_exe, d=self.input, convert=True, f=prank_number, o='"%s"' % self.output, ) self.assertEqual( str(cmdline), _escape_filename(prank_exe) + " -d=%s" % self.input + ' -o="%s"' % self.output + " -f=%i" % prank_number + " -convert", ) self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) message, error = cmdline() self.assertIn("PRANK", message) self.assertTrue( ("converting '%s' to '%s'" % (self.input, filename)) in message, message ) self.assertEqual(error, "") self.assertTrue(os.path.isfile(filename)) old = AlignIO.read(self.input, "fasta") # Hack... if format == "phylip": for record in old: record.id = record.id[:10] new = AlignIO.read(filename, format) self.assertEqual(len(old), len(new)) for old_r, new_r in zip(old, new): self.assertEqual(old_r.id, new_r.id) self.assertEqual(str(old_r.seq), str(new_r.seq)) os.remove(filename) def test_convert_to_fasta(self): """Convert FASTA to FASTA format.""" self.conversion(8, "fas", "fasta") # Prank v.100701 seems to output an invalid file here... # def test_convert_to_phylip32(self): # """Convert FASTA to PHYLIP 3.2 format.""" # self.conversion(11, "phy", "phylip") def test_convert_to_phylip(self): """Convert FASTA to PHYLIP format.""" self.conversion(12, "phy", "phylip") # PRANK truncated the record names in the matrix block. An error? # def test_convert_to_paup_nexus(self): # """Convert FASTA to PAUP/NEXUS.""" # self.conversion(17, "nex", "nexus") # We don't support format 18, PAML if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)