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src/c/o/cogent-1.5.3/cogent/app/dotur.py   cogent(Download)
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.format.table import phylipMatrix
from cogent.parse.dotur import OtuListParser
 
__author__ = "Jeremy Widmann"
    res = app(phylip_matrix_string)
 
    otu_list = OtuListParser(res['List'].readlines())
 
    #remap sequence names
    res = app(d_matrix_string)
 
    otu_list = OtuListParser(res['List'].readlines())
 
    shutil.rmtree(app.WorkingDir)

src/p/y/pycogent-HEAD/cogent/app/dotur.py   pycogent(Download)
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.format.table import phylipMatrix
from cogent.parse.dotur import OtuListParser
 
__author__ = "Jeremy Widmann"
    res = app(phylip_matrix_string)
 
    otu_list = OtuListParser(res['List'].readlines())
 
    #remap sequence names
    res = app(d_matrix_string)
 
    otu_list = OtuListParser(res['List'].readlines())
 
    shutil.rmtree(app.WorkingDir)

src/p/y/pycogent-HEAD/tests/test_parse/test_dotur.py   pycogent(Download)
#!/usr/bin/env python
# test_dotur.py
 
from cogent.util.unit_test import TestCase, main
from cogent.parse.dotur import get_otu_lists, OtuListParser
    def test_otulistparser_no_data(self):
        """OtuListParser should return correct result given no data.
        """
        res = OtuListParser([])
        self.assertEqual(list(res),[])
 
    def test_otulistparser_parser(self):
        """OtuListParser should return correct result given basic output.
        """
        res = OtuListParser(self.otu_list_string.split('\n'))

src/p/y/pycogent-HEAD/tests/test_app/test_dotur.py   pycogent(Download)
from cogent.app.dotur import Dotur, dotur_from_alignment, dotur_from_file,\
    remap_seq_names
from cogent.parse.dotur import OtuListParser
 
__author__ = "Jeremy Widmann"

src/c/o/cogent-1.5.3/tests/test_parse/test_dotur.py   cogent(Download)
#!/usr/bin/env python
# test_dotur.py
 
from cogent.util.unit_test import TestCase, main
from cogent.parse.dotur import get_otu_lists, OtuListParser
    def test_otulistparser_no_data(self):
        """OtuListParser should return correct result given no data.
        """
        res = OtuListParser([])
        self.assertEqual(list(res),[])
 
    def test_otulistparser_parser(self):
        """OtuListParser should return correct result given basic output.
        """
        res = OtuListParser(self.otu_list_string.split('\n'))

src/c/o/cogent-1.5.3/tests/test_app/test_dotur.py   cogent(Download)
from cogent.app.dotur import Dotur, dotur_from_alignment, dotur_from_file,\
    remap_seq_names
from cogent.parse.dotur import OtuListParser
 
__author__ = "Jeremy Widmann"