def test_newtree(self):
"""Test newtree files."""
input_file = "Registry/seqs.fasta"
output_file = "temp_test.aln"
newtree_file = "temp_test.dnd"
cline = ClustalwCommandline(
clustalw_exe, infile=input_file, outfile=output_file, newtree=newtree_file, align=True
)
self.standard_test_procedure(cline)
cline.newtree = "temp with space.dnd"
self.standard_test_procedure(cline)
def test_newtree(self):
"""Test newtree files."""
input_file = "Registry/seqs.fasta"
output_file = "temp_test.aln"
newtree_file = "temp_test.dnd"
cline = ClustalwCommandline(clustalw_exe,
infile=input_file,
outfile=output_file,
newtree=newtree_file,
align=True)
self.standard_test_procedure(cline)
cline.newtree = "temp with space.dnd"
self.standard_test_procedure(cline)
print "Calling clustalw on %s (with %i records)" % (repr(input_file), len(input_records))
print "using output file %s" % repr(output_file)
if newtree_file is not None:
print "requesting output guide tree file %s" % repr(newtree_file)
# Any filenames with spaces should get escaped with quotes automatically.
# Using keyword arguments here.
if clustalw_exe == "clustalw2":
# By using the stats keyword, we require ClustalW 2.0.10 or higher.
cline = ClustalwCommandline(clustalw_exe, infile=input_file, outfile=output_file, stats=statistics_file)
else:
cline = ClustalwCommandline(clustalw_exe, infile=input_file, outfile=output_file)
assert str(eval(repr(cline))) == str(cline)
if newtree_file is not None:
# Test using a property:
cline.newtree = newtree_file
# I don't just want the tree, also want the alignment:
cline.align = True
assert str(eval(repr(cline))) == str(cline)
output, error = cline()
assert output.strip().startswith("CLUSTAL")
assert error.strip() == ""
# Check the output...
align = AlignIO.read(output_file, "clustal")
# The length of the alignment will depend on the version of clustalw
# (clustalw 2.0.10 and clustalw 1.83 are certainly different).
print "Got an alignment, %i sequences" % (len(align))
if clustalw_exe == "clustalw2":
assert os.path.isfile(statistics_file)
os.remove(statistics_file)
output_records = SeqIO.to_dict(SeqIO.parse(output_file, "clustal"))
os.remove(output_file)
print "Calling clustalw on %s (with %i records)" \
% (repr(input_file), len(input_records))
print "using output file %s" % repr(output_file)
if newtree_file is not None:
print "requesting output guide tree file %s" % repr(newtree_file)
#Any filesnames with spaces should get escaped with quotes automatically.
#Using keyword arguments here.
cline = ClustalwCommandline(clustalw_exe,
infile=input_file,
outfile=output_file)
assert str(eval(repr(cline))) == str(cline)
if newtree_file is not None:
#Test using a property:
cline.newtree = newtree_file
#I don't just want the tree, also want the alignment:
cline.align = True
assert str(eval(repr(cline))) == str(cline)
#print cline
output, error = cline()
assert output.strip().startswith("CLUSTAL")
assert error.strip() == ""
#Check the output...
align = AlignIO.read(output_file, "clustal")
#The length of the alignment will depend on the version of clustalw
#(clustalw 2.0.10 and clustalw 1.83 are certainly different).
print "Got an alignment, %i sequences" % (len(align))
output_records = SeqIO.to_dict(SeqIO.parse(output_file, "clustal"))
assert set(input_records.keys()) == set(output_records.keys())
for record in align:
