Python split_taxonomy_list示例

示例#1

文件： split_taxonomy_script.py 项目： phinna/hmm-tax

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)

示例#2

文件： split_taxonomy.py 项目： johnchase/hmm-tax

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)

示例#3

文件： TestFile.py 项目： phinna/hmm-tax

    def test_assign_otuID_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_otuID_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()