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test_Prank_tool.py
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test_Prank_tool.py
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"""
Unittests for Bio.Align.Applications interface for PRANK
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.
"""
import sys
import os
import unittest
from Bio import Application
from Bio import AlignIO
from Bio import SeqIO
from Bio import MissingExternalDependencyError
from Bio.Align.Applications import PrankCommandline
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 :
import commands
output = commands.getoutput("prank")
if "not found" not in output and "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):
"""
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), prank_exe + " -d=Fasta/fa01")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEqual(result.return_code, 0)
self.assert_("Total time" in stdout.read())
self.assertEqual(stderr.read(), "")
self.assertEqual(str(result._cl), str(cmdline))
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(open(self.infile1),"fasta"))
#Try using keyword argument,
cmdline = PrankCommandline(prank_exe, d=self.infile1, noxml=True)
#Try using a property,
cmdline.d = self.infile1
cmdline.f = 17 # NEXUS format
cmdline.set_parameter("notree", True)
self.assertEqual(str(cmdline), prank_exe + \
" -d=Fasta/fa01 -f=17 -noxml -notree")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEqual(result.return_code, 0)
self.assert_("Total time" in stdout.read())
self.assertEqual(stderr.read(), "")
self.assertEqual(str(result._cl), str(cmdline))
out_handle = open("output.2.nex", "r")
align = AlignIO.read(out_handle, "nexus")
out_handle.close()
for old, new in zip(records, align) :
#Prank automatically reduces name to 9 chars
self.assertEqual(old.id[:9], new.id)
#infile1 has alignment gaps in it
self.assertEqual(str(new.seq).replace("-",""),
str(old.seq).replace("-",""))
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("-noxml", True)
cmdline.set_parameter("notree", True)
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), prank_exe + " -d=Fasta/fa01 -noxml" + \
" -notree -dots -gaprate=0.321 -gapext=0.6 -kappa=3" + \
" -once -skipins -realbranches")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEqual(result.return_code, 0)
self.assert_("Total time" in stdout.read())
self.assertEqual(stderr.read(), "")
self.assertEqual(str(result._cl), str(cmdline))
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), prank_exe \
+ ' -d=%s' % self.input \
+ ' -o="%s"' % self.output \
+ ' -f=%i' % prank_number \
+ ' -convert')
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEqual(result.return_code, 0)
message = stdout.read().strip()
self.assert_(("PRANK: converting '%s' to '%s'" % (self.input, filename)) \
in message, message)
self.assertEqual(stderr.read(), "")
self.assertEqual(str(result._cl), str(cmdline))
self.assert_(os.path.isfile(filename))
old = AlignIO.read(open(self.input), "fasta")
#Hack...
if format=="phylip" :
for record in old :
record.id = record.id[:10]
new = AlignIO.read(open(filename), format)
assert 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_ig(self):
"""Convert FASTA to Inteligenetics format."""
self.conversion(1, "igs", "ig")
#Works, but parsing gives a user warning due to malformed LOCUS line
#def test_convert_to_genbank(self):
# """Convert FASTA to GenBank."""
# self.conversion(2, "gen", "genbank")
def test_convert_to_nbrf(self):
"""Convert FASTA to NBRF/PIR format."""
self.conversion(3, "nbr", "pir")
#Our EMBL parser doesn't (yet) support the minimal ID line format used
#def test_convert_to_genbank(self):
# """Convert FASTA to EMBL."""
# self.conversion(4, "emb", "embl")
def test_convert_to_fasta(self):
"""Convert FASTA to FASTA format."""
self.conversion(8, "fas", "fasta")
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")
#This isn't the NBRF/PIR format, what ever it is, we don't support it yet:
#def test_convert_to_pir_codata(self):
# """Convert FASTA to PIR/CODATA."""
# self.conversion(14, "pir", "???")
#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")
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)