def test_TCoffee_3(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.phy "
"-type protein -outorder input -gapopen -2 -gapext -5")
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_(child.stderr.read().strip().startswith("PROGRAM: T-COFFEE"))
align = AlignIO.read(open(self.outfile4), "clustal")
records = list(SeqIO.parse(open(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("-",""))
del child
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_2(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_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_2(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")
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEquals(result.return_code, 0)
self.assertEquals(stderr.read(), "")
align = AlignIO.read(open(self.outfile3), "pir")
records = list(SeqIO.parse(open(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_2(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")
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEquals(result.return_code, 0)
self.assertEquals(stderr.read(), "")
align = AlignIO.read(open(self.outfile3), "pir")
records = list(SeqIO.parse(open(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_3(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.phy "
"-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_3(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.phy "
"-outorder input -gapopen -2 -gapext -5")
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEquals(result.return_code, 0)
self.assert_(stderr.read().strip().startswith("PROGRAM: T-COFFEE"))
align = AlignIO.read(open(self.outfile4), "clustal")
records = list(SeqIO.parse(open(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_2(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")
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.assertEquals(child.stderr.read(), "")
align = AlignIO.read(open(self.outfile3), "pir")
records = list(SeqIO.parse(open(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("-",""))
del child