Python assign_seqID_to_seqs примеры использования

Пример #1

Файл: TestFile.py Проект: johnchase/hmm-tax

    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()

Пример #2

Файл: split_taxonomy.py Проект: 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)