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.assertTrue("Total time" in 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_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_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, noxml=True)
#Try using a property,
cmdline.d = self.infile1
cmdline.f = 17 # NEXUS format
cmdline.set_parameter("notree", True)
self.assertEqual(
str(cmdline),
_escape_filename(prank_exe) +
" -d=Fasta/fa01 -f=17 -noxml -notree")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
stdout, stderr = cmdline()
self.assertTrue("Total time" in stdout)
self.assertEqual(stderr, "")
try:
align = AlignIO.read("output.2.nex", "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_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_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))
child = subprocess.Popen(
str(cmdline), stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform != "win32")
)
return_code = child.wait()
self.assertEqual(return_code, 0)
self.assert_("Total time" in child.stdout.read())
self.assertEqual(child.stderr.read(), "")
align = AlignIO.read(open("output.2.nex"), "nexus")
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("-", ""))
del child
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, noxml=True)
#Try using a property,
cmdline.d = self.infile1
cmdline.f = 17 # NEXUS format
cmdline.set_parameter("notree", True)
self.assertEqual(str(cmdline), _escape_filename(prank_exe) +
" -d=Fasta/fa01 -f=17 -noxml -notree")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
stdout, stderr = cmdline()
self.assertTrue("Total time" in stdout)
self.assertEqual(stderr, "")
try:
align = AlignIO.read("output.2.nex", "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_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.assertTrue("Total time" in output)
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))
output, error = cmdline()
self.assertEqual(error, "")
self.assertTrue("Total time" in output)
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(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(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))
child = subprocess.Popen(
str(cmdline), stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform != "win32")
)
return_code = child.wait()
self.assertEqual(return_code, 0)
self.assert_("Total time" in child.stdout.read())
self.assertEqual(child.stderr.read(), "")
del child
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_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))
child = subprocess.Popen(str(cmdline),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform!="win32"))
return_code = child.wait()
self.assertEqual(return_code, 0)
self.assertTrue("Total time" in child.stdout.read())
self.assertEqual(child.stderr.read(), "")
try:
align = AlignIO.read(open("output.2.nex"), "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
del child
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.assertTrue("Total time" in stdout, stdout)
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.assertTrue("Total time" in stdout, stdout)
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))
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))
child = subprocess.Popen(
str(cmdline), stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform != "win32")
)
return_code = child.wait()
self.assertEqual(return_code, 0)
self.assert_("Total time" in child.stdout.read())
self.assertEqual(child.stderr.read(), "")
del child
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))
