def test_newtree_files(self):
"""Test requesting a guide tree."""
input_file = "Fasta/f002"
output_file = "temp_test.aln"
newtree_file = "temp_test.dnd"
cline = ClustalOmegaCommandline(
clustalo_exe, infile=input_file, outfile=output_file, guidetree_out=newtree_file, outfmt="clustal"
)
self.standard_test_procedure(cline)
cline.guidetree_out = "temp with space.dnd"
self.standard_test_procedure(cline)
def test_newtree_files(self):
"""Test requesting a guide tree."""
input_file = "Fasta/f002"
output_file = "temp_test.aln"
newtree_file = "temp_test.dnd"
cline = ClustalOmegaCommandline(clustalo_exe,
infile=input_file,
outfile=output_file,
guidetree_out=newtree_file,
outfmt="clustal")
self.standard_test_procedure(cline)
cline.guidetree_out = "temp with space.dnd"
self.standard_test_procedure(cline)
% (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, force=True to over-write the output file.
cline = ClustalOmegaCommandline(clustalo_exe,
infile=input_file,
outfile=output_file,
outfmt="clustal",
force=True)
assert str(eval(repr(cline)))==str(cline)
if newtree_file is not None:
#Test using a property:
cline.guidetree_out = newtree_file
assert str(eval(repr(cline)))==str(cline)
#print cline
output, error = cline()
#assert output, "No output from: %s\n%s" % (cline, error)
assert not output or output.strip().startswith("CLUSTAL"), output
assert error.strip() == "" or \
error.startswith("WARNING: Sequence type is DNA."), error
#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 len(set(input_records.keys())) == len(set(output_records.keys())), \
"%r vs %r" %(sorted(input_records.keys()), sorted(output_records.keys()))
