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src/c/o/cogent-1.5.3/cogent/app/mothur.py   cogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath, \
    CommandLineAppResult, ApplicationError
from cogent.parse.mothur import parse_otu_list
 
 
def mothur_from_file(file):
    app = Mothur(InputHandler='_input_as_lines')
    result = app(file)
    # Force evaluation, so we can safely clean up files
    otus = list(parse_otu_list(result['otu list']))

src/q/i/qiime-1.8.0/qiime/pycogent_backports/mothur.py   qiime(Download)
 
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.mothur import parse_otu_list
 
 
def mothur_from_file(file):
    app = Mothur(InputHandler='_input_as_lines')
    result = app(file)
    # Force evaluation, so we can safely clean up files
    otus = list(parse_otu_list(result['otu list']))

src/p/y/pycogent-HEAD/cogent/app/mothur.py   pycogent(Download)
 
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.mothur import parse_otu_list
 
 
def mothur_from_file(file):
    app = Mothur(InputHandler='_input_as_lines')
    result = app(file)
    # Force evaluation, so we can safely clean up files
    otus = list(parse_otu_list(result['otu list']))

src/q/i/qiime-1.8.0/qiime/pick_otus.py   qiime(Download)
 
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.mothur import parse_otu_list as mothur_parse
from cogent.app.cd_hit import cdhit_clusters_from_seqs
from cogent.app.mothur import Mothur
        app.Parameters['method'].on(self.Params['Algorithm'])
        results = app(seq_path)
        parsed_otus = mothur_parse(results['otu list'])
        clusters = self.__pick_clusters(parsed_otus)
        results.cleanUp()

src/p/y/pycogent-HEAD/tests/test_parse/test_mothur.py   pycogent(Download)
 
from cogent.util.unit_test import TestCase, main
from cogent.parse.mothur import parse_otu_list
 
class FunctionTests(TestCase):
    def test_parse_otu_list(self):
        observed = list(parse_otu_list(StringIO(mothur_output)))

src/c/o/cogent-1.5.3/tests/test_parse/test_mothur.py   cogent(Download)
 
from cogent.util.unit_test import TestCase, main
from cogent.parse.mothur import parse_otu_list
 
class FunctionTests(TestCase):
    def test_parse_otu_list(self):
        observed = list(parse_otu_list(StringIO(mothur_output)))