Did I find the right examples for you? yes no

All Samples(18)  |  Call(10)  |  Derive(0)  |  Import(8)

src/c/o/cogent-1.5.3/cogent/motif/k_word.py   cogent(Download)
#!/usr/bin/env python
"""MotifFinder that searches for over-represented k-words in an alignment."""
 
from __future__ import division
from cogent.motif.util import Motif, Module, ModuleFinder, ModuleConsolidator, \
        """
        #Create new MotifResults object
        k_word_results = MotifResults()
        k_word_results.Modules=[]
        k_word_results.Motifs=[]

src/p/y/pycogent-HEAD/cogent/motif/k_word.py   pycogent(Download)
#!/usr/bin/env python
"""MotifFinder that searches for over-represented k-words in an alignment."""
 
from __future__ import division
from cogent.motif.util import Motif, Module, ModuleFinder, ModuleConsolidator, \
        """
        #Create new MotifResults object
        k_word_results = MotifResults()
        k_word_results.Modules=[]
        k_word_results.Motifs=[]

src/c/o/cogent-1.5.3/tests/test_motif/test_util.py   cogent(Download)
#!/usr/bin/env python
#file cogent_tests/motif/test_util.py
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
        results = {'key1':'value1','key2':'value2'}
        parameters = {'parameter1':1,'parameter2':2}
        mr = MotifResults([module],[motif],results,parameters)
        self.assertEqual(mr.Modules,[module])
        self.assertEqual(mr.Motifs,[motif])
                    ]
        self.motifs_with_ids = map(Motif,self.modules_with_ids)
        self.motif_results = MotifResults(Modules=self.modules_with_ids,\
            Motifs=self.motifs_with_ids)
 

src/p/y/pycogent-HEAD/tests/test_motif/test_util.py   pycogent(Download)
#!/usr/bin/env python
#file cogent_tests/motif/test_util.py
from __future__ import division
from cogent.util.unit_test import TestCase, main
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
        results = {'key1':'value1','key2':'value2'}
        parameters = {'parameter1':1,'parameter2':2}
        mr = MotifResults([module],[motif],results,parameters)
        self.assertEqual(mr.Modules,[module])
        self.assertEqual(mr.Motifs,[motif])
                    ]
        self.motifs_with_ids = map(Motif,self.modules_with_ids)
        self.motif_results = MotifResults(Modules=self.modules_with_ids,\
            Motifs=self.motifs_with_ids)
 

src/c/o/cogent-1.5.3/cogent/parse/meme.py   cogent(Download)
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.parse.record import DelimitedSplitter
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
     MotifResults, make_remap_dict
from cogent.core.moltype import DNA, RNA, PROTEIN
    warnings = []
    #Create MotifResults object
    meme_motif_results = MotifResults()
    #Get main block and alphabet
    main_block, alphabet = getDataBlock(lines)

src/p/y/pycogent-HEAD/cogent/parse/meme.py   pycogent(Download)
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.parse.record import DelimitedSplitter
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
     MotifResults, make_remap_dict
from cogent.core.moltype import DNA, RNA, PROTEIN
    warnings = []
    #Create MotifResults object
    meme_motif_results = MotifResults()
    #Get main block and alphabet
    main_block, alphabet = getDataBlock(lines)

src/c/o/cogent-1.5.3/cogent/parse/gibbs.py   cogent(Download)
 
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
     MotifResults
from cogent.core.moltype import DNA, RNA, PROTEIN
            return None
    #Create MotifResults object
    gibbs_motif_results = MotifResults()
 
    #Get sequence map

src/p/y/pycogent-HEAD/cogent/parse/gibbs.py   pycogent(Download)
 
from cogent.parse.record_finder import LabeledRecordFinder
from cogent.motif.util import Location, ModuleInstance, Module, Motif,\
     MotifResults
from cogent.core.moltype import DNA, RNA, PROTEIN
            return None
    #Create MotifResults object
    gibbs_motif_results = MotifResults()
 
    #Get sequence map