def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if isdir(opts.otu_table_fp):
ret_code = create_dir(opts.output_fp, fail_on_exist=False)
# run on each file in dir
for fp in glob(opts.otu_table_fp + '/*biom'):
parent_dir_name, file_name = split(fp)
basename, extension = splitext(file_name)
out_fp = opts.output_fp + "/" + basename + "_shared_OTUs.txt"
with open(out_fp, 'w') as out_fh:
out_fh.write(calc_shared_phylotypes(load_table(fp),
opts.reference_sample))
else:
# run in single file mode
try:
out_fh = open(opts.output_fp, "w")
except IOError as message:
exit(("Can't open output file %s for writing. Check the "
"permissions or existing directory with identical "
"name.\n%s") % (opts.output_fp, message))
out_fh.write(calc_shared_phylotypes(load_table(opts.otu_table_fp),
opts.reference_sample))
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if isdir(opts.otu_table_fp):
ret_code = create_dir(opts.output_fp, fail_on_exist=False)
# run on each file in dir
for fp in glob(opts.otu_table_fp + '/*biom'):
parent_dir_name, file_name = split(fp)
basename, extension = splitext(file_name)
out_fp = opts.output_fp + "/" + basename + "_shared_OTUs.txt"
with open(out_fp, 'w') as out_fh:
out_fh.write(
calc_shared_phylotypes(load_table(fp),
opts.reference_sample))
else:
# run in single file mode
try:
out_fh = open(opts.output_fp, "w")
except IOError as message:
exit(("Can't open output file %s for writing. Check the "
"permissions or existing directory with identical "
"name.\n%s") % (opts.output_fp, message))
out_fh.write(
calc_shared_phylotypes(load_table(opts.otu_table_fp),
opts.reference_sample))
def test_calc_shared_phylotypes(self):
"""calc_shared_phylotypes computes correct matrix"""
observed = calc_shared_phylotypes(self.biom_as_string)
expected = """\tS1\tS2\tS3
S1\t5\t2\t3
S2\t2\t2\t1
S3\t3\t1\t3\n"""
self.assertEqual(observed, expected)
def test_calc_shared_phylotypes(self):
"""calc_shared_phylotypes computes correct matrix"""
observed = calc_shared_phylotypes(self.biom_as_string)
expected = """\tS1\tS2\tS3
S1\t5\t2\t3
S2\t2\t2\t1
S3\t3\t1\t3\n"""
self.assertEqual(observed, expected)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if exists(opts.output_fp) and not opts.force_overwrite:
exit("Output file already exists. Choose another output "
+"filename or use options --force_overwrite")
if isdir(opts.otu_table_fp):
ret_code = create_dir(opts.output_fp, fail_on_exist=False)
if ret_code != 0:
if ret_code==1 and opts.force_overwrite:
#dir exists, ovewrite
pass
else:
exit("Failed to make output dir, Check permissions and "
+"check for file with identical name")
#run on each file in dir
for fp in glob(opts.otu_table_fp +'/*'):
parent_dir_name, file_name = split(fp)
basename, extension = splitext(file_name)
out_fp = opts.output_fp +"/"+basename+"_shared_OTUs.txt"
out_fh = open(out_fp, "w")
out_fh.write(calc_shared_phylotypes(open(fp, "U"),
opts.reference_sample))
out_fh.close()
else:
#run in single file mode
try:
out_fh = open(opts.output_fp,"w")
except IOError, message:
exit(("Can't open output file %s for writing. Check the permissions "\
+"or existing directory with identical name.\n%s")
% (opts.output_fp,message))
out_fh.write(calc_shared_phylotypes(open(opts.otu_table_fp, "U"),
opts.reference_sample))
