def test_water_file2(self):
"""Run water with the asis trick and nucleotide FASTA file, output to a file."""
# Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(
query,
SeqIO.parse(in_file, "fasta"),
AlignIO.parse(out_file, "emboss"),
local=True,
)
# Clean up,
os.remove(out_file)
def test_water_file3(self):
"""Run water with the asis trick and GenBank file, output to a file."""
# Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
# TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(
query,
SeqIO.parse(in_file, "genbank"),
AlignIO.parse(out_file, "emboss"),
local=True,
)
# Clean up,
os.remove(out_file)
def test_water_file3(self):
"""water with the asis trick and GenBank file, output to a file."""
# Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
# TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(in_file, "genbank"),
AlignIO.parse(out_file, "emboss"),
local=True)
# Clean up,
os.remove(out_file)
def test_water_file2(self):
"""water with the asis trick and nucleotide FASTA file, output to a file."""
#Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"),
errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0: print >> sys.stderr, "\n%s" % cline
self.assertEqual(result.return_code, 0)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file), "fasta"),
AlignIO.parse(open(out_file), "emboss"),
local=True)
#Clean up,
os.remove(out_file)
def test_water_file2(self):
"""water with the asis trick and nucleotide FASTA file, output to a file."""
# Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(in_file, "fasta"),
AlignIO.parse(out_file, "emboss"),
local=True)
# Clean up,
os.remove(out_file)
def test_water_file3(self):
"""water with the asis trick and GenBank file, output to a file."""
#Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
#TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"),
errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0: print >> sys.stderr, "\n%s" % cline
self.assertEqual(result.return_code, 0)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file), "genbank"),
AlignIO.parse(open(out_file), "emboss"),
local=True)
#Clean up,
os.remove(out_file)
def test_water_file3(self):
"""water with the asis trick and GenBank file, output to a file."""
#Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file) :
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
#TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"), errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0 : print >> sys.stderr, "\n%s"%cline
self.assertEqual(result.return_code, 0)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file),"genbank"),
AlignIO.parse(open(out_file),"emboss"),
local=True)
#Clean up,
os.remove(out_file)
def test_water_file(self):
"""water with the asis trick, output to a file."""
#Setup, try a mixture of keyword arguments and later additions:
cline = WaterCommandline(cmd=exes["water"],
gapopen="10",
gapextend="0.5")
#Try using both human readable names, and the literal ones:
cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
#Try using a property set here:
cline.outfile = "Emboss/temp with space.water"
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"),
errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0: print >> sys.stderr, "\n%s" % cline
self.assertEqual(result.return_code, 0)
filename = result.get_result("outfile")
self.assertEqual(filename, "Emboss/temp with space.water")
assert os.path.isfile(filename)
#Check we can parse the output...
align = AlignIO.read(open(filename), "emboss")
self.assertEqual(len(align), 2)
self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
#Clean up,
os.remove(filename)
def test_water_file2(self):
"""water with the asis trick and nucleotide FASTA file, output to a file."""
#Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file) :
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"), errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0 : print >> sys.stderr, "\n%s"%cline
self.assertEqual(result.return_code, 0)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file),"fasta"),
AlignIO.parse(open(out_file),"emboss"),
local=True)
#Clean up,
os.remove(out_file)
def test_water_file(self):
"""water with the asis trick, output to a file."""
#Setup, try a mixture of keyword arguments and later additions:
cline = WaterCommandline(cmd=exes["water"],
gapopen="10", gapextend="0.5")
#Try using both human readable names, and the literal ones:
cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
#Try using a property set here:
cline.outfile = "Emboss/temp with space.water"
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"), errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0 : print >> sys.stderr, "\n%s"%cline
self.assertEqual(result.return_code, 0)
filename = result.get_result("outfile")
self.assertEqual(filename, "Emboss/temp with space.water")
assert os.path.isfile(filename)
#Check we can parse the output...
align = AlignIO.read(open(filename),"emboss")
self.assertEqual(len(align), 2)
self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
#Clean up,
os.remove(filename)
def test_water_file(self):
"""Run water with the asis trick, output to a file."""
# Setup, try a mixture of keyword arguments and later additions:
cline = WaterCommandline(cmd=exes["water"], gapopen="10", gapextend="0.5")
# Try using both human readable names, and the literal ones:
cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
# Try using a property set here:
cline.outfile = "Emboss/temp with space.water"
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output...
align = AlignIO.read(cline.outfile, "emboss")
self.assertEqual(len(align), 2)
self.assertEqual(align[0].seq, "ACCCGGGCGCGGT")
self.assertEqual(align[1].seq, "ACCCGAGCGCGGT")
# Clean up,
os.remove(cline.outfile)
def test_water_file(self):
"""water with the asis trick, output to a file."""
# Setup, try a mixture of keyword arguments and later additions:
cline = WaterCommandline(cmd=exes["water"], gapopen="10", gapextend="0.5")
# Try using both human readable names, and the literal ones:
cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
# Try using a property set here:
cline.outfile = "Emboss/temp with space.water"
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output...
align = AlignIO.read(open(cline.outfile), "emboss")
self.assertEqual(len(align), 2)
self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
# Clean up,
os.remove(cline.outfile)
def test_water_file4(self):
"""Run water with the asis trick and SwissProt file, output to a file."""
# Setup,
query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
out_file = "Emboss/temp_test4.water"
in_file = "SwissProt/P0A186.txt"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
# EMBOSS should work this out, but let's be explicit:
cline.set_parameter("-sprotein", True)
# TODO - Tell water this is a SwissProt file!
cline.set_parameter("-gapopen", "20")
cline.set_parameter("-gapextend", "5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(
query,
SeqIO.parse(in_file, "swiss"),
AlignIO.parse(out_file, "emboss"),
local=True,
)
# Clean up,
os.remove(out_file)
def test_water_file4(self):
"""water with the asis trick and SwissProt file, output to a file."""
# Setup,
query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
out_file = "Emboss/temp_test4.water"
in_file = "SwissProt/sp004"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
# EMBOSS should work this out, but let's be explicit:
cline.set_parameter("-sprotein", True)
# TODO - Tell water this is a SwissProt file!
cline.set_parameter("-gapopen", "20")
cline.set_parameter("-gapextend", "5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(in_file, "swiss"),
AlignIO.parse(out_file, "emboss"),
local=True)
# Clean up,
os.remove(out_file)
def test_water_file4(self):
"""water with the asis trick and SwissProt file, output to a file."""
#Setup,
query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
out_file = "Emboss/temp_test4.water"
in_file = "SwissProt/sp004"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
#EMBOSS should work this out, but let's be explicit:
cline.set_parameter("-sprotein", True)
#TODO - Tell water this is a SwissProt file!
cline.set_parameter("-gapopen", "20")
cline.set_parameter("-gapextend", "5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"),
errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0: print >> sys.stderr, "\n%s" % cline
self.assertEqual(result.return_code, 0)
#Should be able to access this via any alias:
self.assertEqual(result.get_result("-outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file), "swiss"),
AlignIO.parse(open(out_file), "emboss"),
local=True)
#Clean up,
os.remove(out_file)
def test_water_file4(self):
"""water with the asis trick and SwissProt file, output to a file."""
#Setup,
query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
out_file = "Emboss/temp_test4.water"
in_file = "SwissProt/sp004"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file) :
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
#EMBOSS should work this out, but let's be explicit:
cline.set_parameter("-sprotein", True)
#TODO - Tell water this is a SwissProt file!
cline.set_parameter("-gapopen", "20")
cline.set_parameter("-gapextend", "5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"), errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0 : print >> sys.stderr, "\n%s"%cline
self.assertEqual(result.return_code, 0)
#Should be able to access this via any alias:
self.assertEqual(result.get_result("-outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file),"swiss"),
AlignIO.parse(open(out_file),"emboss"),
local=True)
#Clean up,
os.remove(out_file)
