def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
map_file_name, otu_file_name, valid_states_str, num_seqs_per_otu = \
opts.map_fname, opts.otu_table_fp, opts.valid_states, \
opts.num_seqs_per_otu
map_infile = open(map_file_name, 'U')
otu_infile = open(otu_file_name, 'U')
map_out_fname = opts.map_out_fname
otu_out_fname = opts.otu_out_fname
if map_out_fname is None and otu_out_fname is None:
map_out_fname = map_file_name + '.filtered.xls'
otu_out_fname = otu_file_name + '.filtered.xls'
elif otu_out_fname is None:
otu_out_fname = map_out_fname + '-otu.filtered.xls'
elif map_out_fname is None:
map_out_fname = otu_out_fname + '-map.filtered.xls'
# write out the filtered mapping file
map_outfile = open(map_out_fname, 'w')
otu_outfile = open(otu_out_fname, 'w')
filter_otus_and_map(map_infile, otu_infile, map_outfile, otu_outfile,
valid_states_str, num_seqs_per_otu)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
otu_table_fp = opts.otu_table_fp
mapping_fp = opts.mapping_fp
mapping_field = opts.mapping_field
output_dir = opts.output_dir
otu_table_base_name = splitext(split(otu_table_fp)[1])[0]
mapping_data, headers, comments = parse_mapping_file(open(mapping_fp,'U'))
try:
field_index = headers.index(mapping_field)
except ValueError:
option_parser.error("Field is not in mapping file (search is case "+\
"and white-space sensitive). \n\tProvided field: "+\
"%s. \n\tValid fields: %s" % (mapping_field,' '.join(headers)))
mapping_values = set([e[field_index] for e in mapping_data])
create_dir(output_dir)
for v in mapping_values:
v_fp_str = v.replace(' ','_')
otu_table_output_fp = join(output_dir,'%s_%s.txt' % (otu_table_base_name, v_fp_str))
mapping_output_fp = join(output_dir,'mapping_%s.txt' % v_fp_str)
filter_otus_and_map(open(mapping_fp,'U'),
open(otu_table_fp,'U'),
open(mapping_output_fp,'w'),
open(otu_table_output_fp,'w'),
valid_states_str="%s:%s" % (mapping_field,v),
num_seqs_per_otu=1)
def get_result(valid_states_str, num_seqs_per_otu):
otu_infile = StringIO(self.otu_tax_str)
map_infile = StringIO(self.map_str)
otu_outfile = StringIO('')
map_outfile = StringIO('')
filter_otus_and_map(map_infile, otu_infile, map_outfile, otu_outfile,
valid_states_str, num_seqs_per_otu)
otu_outfile.seek(0)
map_outfile.seek(0)
return otu_outfile.read(), map_outfile.read()
