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)