def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if not isfile(opts.input_path):
raise IOError("Input path (%s) not valid. Does it exist?" %
opts.input_path)
samples, otus, data = parse_trflp(open(opts.input_path, 'U'))
t = Table(data, otus, samples)
write_biom_table(t, opts.output_path)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if not isfile(opts.input_path):
raise IOError(
"Input path (%s) not valid. Does it exist?" %
opts.input_path)
samples, otus, data = parse_trflp(open(opts.input_path, 'U'))
t = Table(data, otus, samples)
write_biom_table(t, opts.output_path)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if not isfile(opts.input_path):
raise IOError, \
"Input path (%s) not valid. Does it exist?" % opts.input_path
samples, otus, data = parse_trflp(open(opts.input_path,'U'))
output_f = open(opts.output_path, 'w')
t = table_factory(data,samples,otus)
output_f.write(format_biom_table(t))
output_f.close()
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if not isfile(opts.input_path):
raise IOError, \
"Input path (%s) not valid. Does it exist?" % opts.input_path
if isfile(opts.output_path):
raise IOError, \
"Output path (%s) already exists. Please " % opts.output_path +\
"remove or specify a different path"
samples, otus, data = parse_trflp(open(opts.input_path,'U'))
output_f = open(opts.output_path, 'w')
output_f.write(format_otu_table(samples,otus,data, comment='Created with %s' % __file__))
output_f.close()
def test_parse_trflp_headerless(self):
""" should return a header and otu_table lists"""
data = \
"""Samp-le 1 1000 2000 3000 4000
Sample 2 2000 3000 4000
Sample 3 3000 4000
Sample 4 4000
Sample_5__ 25 """
samples, otus, data = parse_trflp(data.split('\n'))
samples_exp = ['Samp.le.1', 'Sample.2', 'Sample.3', 'Sample.4', 'Sample.5..']
otus_exp = ['Bin__0', 'Bin__1', 'Bin__2', 'Bin__3']
data_exp = array([[1000, 0, 0, 0, 25],\
[2000, 2000, 0, 0, 0],\
[3000, 3000, 3000, 0, 0],\
[4000, 4000, 4000, 4000, 0]])
self.assertEqual(samples, samples_exp)
self.assertEqual(otus, otus_exp)
self.assertEqual(data, data_exp)
def test_parse_trflp(self):
""" should return a header and otu_table lists"""
data = \
""" Bin (10bp) Bin (20bp) Bin (30bp) Bin (40 bp)
Samp-le 1 1000 2000 3000 4000
Sample 2 2000 3000 4000
Sample 3 3000 4000
Sample 4 4000
Sample 5 25 """
samples, otus, data = parse_trflp(data.split('\n'))
samples_exp = ['Samp.le.1', 'Sample.2', 'Sample.3', 'Sample.4', 'Sample.5']
otus_exp = ['Bin__10bp_', 'Bin__20bp_', 'Bin__30bp_', 'Bin__40_bp_']
data_exp = array([[1000, 0, 0, 0, 25],\
[2000, 2000, 0, 0, 0],\
[3000, 3000, 3000, 0, 0],\
[4000, 4000, 4000, 4000, 0]])
self.assertEqual(samples, samples_exp)
self.assertEqual(otus, otus_exp)
self.assertEqual(data, data_exp)