def test_assign_seqID_to_seqs(self): expected="""\ >822577 AGAGTTTGATCCTGGCTCAGGGTGAACGCTAGTAGTATGCTTAACACATGCGAGTTGAACGAAGATTTATCTTAGTGGCAAACGGGTGAGTAATACATAGGAATCTGCCTTTTAGTACGGGAAAAAATCCTGTATAATACAGTAAAAAACTAAAAAAGAAATATTTTGCTAAAAGATGAGCCTATGCAGGATTAGGTAGTTGGTAAGGTTAAGGCTTACCAAGCCTGTGATCCTTAGTTGTTTTGAGAGATTGAACAACCACACTGGGACTGAGACAAGGCCCAGGCTTCAGTAGAGGCCAGCAGTGAGGAATCTTGGGCAATGAGCGAAAGCTTGACCCAGCAATATTACATGAAGGAAGACTGCTCAAAAGTTGTAAACTTCATTAATTGAGGAGGACGATTGACGTTACTTAATTAACAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAAGACGAAGGGGGCGAGCGTTACCCATGATGACTGGGCGTAAAGGGTCCGTAGGCGGCTTTTTATGTTAAAAGTAAAATCAAAAAGCTTTACTTTTTGAGGCTTTTAATACGTTAGAGCTCGGAGTTTGAAGGAAGATAGTAGAATTTCATATGAAGGGGTGAAATCCGTAGAATTATGAAGGAATACTAAAGGCGAAGGCAACTATCTATTTCAATCTGACGTTGAGGGACGAAAGCATGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCATGCCGTCAAAGATGAGTGCTCTTGTTTGAATTATATTTTGGACAATTAGTTAACACATAAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGACGGAACTCAAAGGAATTGGCGGGGGCCTATACGAGTGGTGGAGCATGTGGTTTAATGCGACAATACGCGCGAAACCTTACCAGTTTTTGATATATATTTTGGATAATCTTTGTGGATAATCAAAAGGATTTATACAGGTGCTGCATGGCTGTCGTCAGCCCGTGTCGTAAGATGTTAGGTTCACTCTTTTTAACGGGCGAAACCCCTGTAGTTAGTTACTATTTATATATCTTATATAAAGGACTTTAACTATACTGCTTTATTGTTTAAATATTTGCTAATTGTAAACAATTAGCAACGTTAAGTGTTATTTTTTTTAAATATATTACTTGTCGTTTCAACTTATTGTTGAGTTTTTATTACAATATATAATGAGGAAGGAGGGGATGACGTCAAGTCTTTATGGCCCTTATGAACTGGGCTACACACGTGCTACAATGGTAAAGACAAAAAGAAGCAATAAGGTAACTTGGAGCTAATCTTAAAAATTTACCAAAGTTCGGATTGTGGGCTGCAACTCGCCCACATGAAGGTGGAATCACTAGTAATCACGAATCAGAACGTCGTGGTGAATTTGTACTTAGGCCTTGTACACACCGCCCGTCACGTGCCGGAAGTCGGCTTGGCTAAAAAATATTTGTTGATTATTGTGTTTAATTTTTTTATTTTTTATGTTAACAAATTTCAAAGTTTACTTTAATTTGCATAATTTATAGTCGGGTTGATAACTGGGATGAAGTCGTAACAAGGTAACC >1837676 AAACAATTAAGAGTTTGATCCTGGCTCTGAGTGAATGCTAGCGGCATGCCTTACACATGCAAGTCGTACGAAATTAATAAAATGATTTCGTGGCGTATAGGTGAGTAAAGTACAAAGCGTGTATGCTAAGTTTAGCTAATACTAAATATATTAACTTAATTAAGTTATTAAAGATTTTTCGCTTAGCAGACATGTTTGTATAGGATTAGGTAGTTGGTGATGGGTTTAGCTCACCAAGCCTACGATCCTTAGCTGGTCTTGGAGGACTATCAGCCACAGCGGGACGGTTACATCCCGAACTTTTTGGCAGCAGTGAGGAATATTGGACAATGGGCGCAAGCTTGATCCAGCAATGCCGCGTGGGTGAGGAAGGCTTAGATTGTAAAATCCTTTCGTCGAAGATGATAATGACAGTATTCGAAAAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAAAACGGAGGGGGCTAGTGTTACTCAACTTGACTGGGCGTAAAGGGCGTGAAGGTGGTATGGTACGTTTTATTGTAAATACTCAAACATAATTTGAGGAGCTTTAAAATACGGCTATGCTTGAGTTTATTTGAAGAAAGTTGTACTTCTAGTGTAGAGGTGAAATTTGCAAAAATTAGAAGGACAGTCCACGGGCGAAAGCGACTTTCTACTATAAACTGACACTATAGCGCGAAAGCATAGGTAGCAAACGGGATTAGAGACCCCGGTAGTCTATGCAGTGACCGATGAATACTAAATGCTCTTATCCGTAAGAGAGTATTTAAGCTAACGCGTAAGTATTCCGCCTGGGAACTACAACCGCAAGGTTCAAACTTAAAGGAATTGACGGAGGGCTATTTCAGCGGTGGAGCATGTGGTTTAATCCGATATACCGCGTAGAACCTTACCAGCTCTTGATGAGCAAATCTGTTTAGGTTTAGAATCCTGAACATTCGTTTTTTTAGCGAAGTATTGGTTTGCACAGGTGTTGCATGGCTGTCGTCAGCTCGTGTTTTGAGATGTTAGGTTAACTCCTTTAACGGGCGCAACCCCCTAGCTTAATTATAAGTTTACTGCTTAGGAAATCTAAGAGGAGGGCAGGGATGATGTCAAGTCGTTATGACCTTTATGGGCTGGGCTACTCACGTGCTACAACGGTACGTACAAAGAGAAGCGAAAACGTAAGTTTTAGCAATACTCAAAAAACGTATCTCAGTTCAGATTGTACCCTGAAAATTGGATACATGAAGTTGGAATCGCTAGTAATCGTGTATCAGAATGGCACGGTGAATACCCCCTCAGCCCTAGTACACACCGCCCGTCACGCGCTGGAAATTAGTTTTGGTTGACATAAGTAGAGGATTATAATTCTTTAAGTCTAATAAAATTTAGTATCTTTAAATTGTTTTATTTTAGATTAAAATTACTGCTTATAACATTAAAGCTAAGGACTGGTGCGAAGTCGTAACAGGGTAGTCGTAGGGGAACCTGCGGCTGGACCA """ self.output_dir=mkdtemp(prefix='TaxonomyTest_') taxonomy_level='5' otu_f_list=[] otu_match_list=[] otu_f_list.append(self.otu_f) otu_match_list.append(self.otu_match_f) sub_taxonomy_list=[] sub_taxonomy=split_taxonomy_list(otu_f_list,taxonomy_level,self.output_dir) sub_taxonomy_list.append(sub_taxonomy) assign_seqID_to_seqs(sub_taxonomy_list,otu_match_list,self.output_dir) output_taxon_fp=os.path.join(self.output_dir,'c_taxonomy','c__Alphaproteobacteria.fasta') result=open(output_taxon_fp,'U') self.assertEqual(result.read(),expected) result.close()
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) sub_taxonomy_list = [] if opts.taxonomy_level == "": 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_seqID_to_seqs(taxon_list, opts.input_fasta_fps, opts.output_dir) else: 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_seqID_to_seqs(sub_taxonomy_list, opts.input_fasta_fps, opts.output_dir)