def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
sub_taxonomy_list=[]
taxonomic_rank_dictionary=create_taxonomic_rank_dictionary(opts.input_taxonomy_fps)
otu_dictionary=create_otu_dictionary(opts.input_fasta_fps)
if opts.taxonomy_level=="":
if path.isdir(opts.output_dir)==False:
mkdir(opts.output_dir,0755)
sub_taxonomy=split_taxonomy_list(opts.input_taxonomy_fps,7,opts.output_dir)
sub_taxonomy_list.append(sub_taxonomy)
assign_otuID_to_seqs(taxonomic_rank_dictionary,otu_dictionary,sub_taxonomy_list,opts.output_dir)
else:
sub_taxonomy=split_taxonomy_list(opts.input_taxonomy_fps,7,opts.output_dir)
sub_taxonomy_list.append(sub_taxonomy)
assign_otuID_to_seqs(taxonomic_rank_dictionary,otu_dictionary,sub_taxonomy_list,opts.output_dir)
else:
if path.isdir(opts.output_dir)==False:
mkdir(opts.output_dir,0755)
sub_taxonomy=split_taxonomy_list(opts.input_taxonomy_fps,opts.taxonomy_level,opts.output_dir)
sub_taxonomy_list.append(sub_taxonomy)
assign_otuID_to_seqs(taxonomic_rank_dictionary,otu_dictionary,sub_taxonomy_list,opts.output_dir)
else:
sub_taxonomy=split_taxonomy_list(opts.input_taxonomy_fps,opts.taxonomy_level,opts.output_dir)
sub_taxonomy_list.append(sub_taxonomy)
assign_otuID_to_seqs(taxonomic_rank_dictionary,otu_dictionary,sub_taxonomy_list,opts.output_dir)
build_cm_models(opts.output_dir)
def test_build_cm_models(self):
sto_dir="/scratch-lt/hhh34/test_infernal"
build_cm_models(sto_dir)
expected_cm_list=[]
for roots,dirs,files in os.walk(sto_dir):
for name in files:
fileName,fileExtension = os.path.splitext(name)
if fileExtension == '.cm':
expected_cm_list.append(fileName+'.cm')
actual=['k__Archaea.cm','k__Bacteria.cm']
self.assertEqual(actual,expected_cm_list)
