Did I find the right examples for you? yes no

All Samples(22)  |  Call(10)  |  Derive(0)  |  Import(12)

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
 
    for ct, module in enumerate(gibbs_motif_results.Modules):
        gibbs_motif_results.Motifs.append(Motif(module))
    gibbs_motif_results.Alphabet=module.Alphabet
    return gibbs_motif_results

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
 
    for ct, module in enumerate(gibbs_motif_results.Modules):
        gibbs_motif_results.Motifs.append(Motif(module))
    gibbs_motif_results.Alphabet=module.Alphabet
    return gibbs_motif_results

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, \
                k_word_results.Modules.append(module)
                #Create a Motif from the module and append to Motifs list
                k_word_results.Motifs.append(Motif(module))
        return k_word_results
 

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, \
                k_word_results.Modules.append(module)
                #Create a Motif from the module and append to Motifs list
                k_word_results.Motifs.append(Motif(module))
        return k_word_results
 

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
                alphabet,remap_dict))
        for module in meme_motif_results.Modules:
            meme_motif_results.Motifs.append(Motif(module))
    return meme_motif_results
 

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
                alphabet,remap_dict))
        for module in meme_motif_results.Modules:
            meme_motif_results.Motifs.append(Motif(module))
    return meme_motif_results
 

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,\
                            ('c',8): ModuleInstance('guc', Location('c',8,10)),
                            })
        m = Motif(module)
        self.assertEqual(m.Modules,[module])
        self.assertEqual(m.Info,None)
                            ('c',8): ModuleInstance('guc', Location('c',8,10)),
                            })
        motif = Motif([module])
        results = {'key1':'value1','key2':'value2'}
        parameters = {'parameter1':1,'parameter2':2}

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,\
                            ('c',8): ModuleInstance('guc', Location('c',8,10)),
                            })
        m = Motif(module)
        self.assertEqual(m.Modules,[module])
        self.assertEqual(m.Info,None)
                            ('c',8): ModuleInstance('guc', Location('c',8,10)),
                            })
        motif = Motif([module])
        results = {'key1':'value1','key2':'value2'}
        parameters = {'parameter1':1,'parameter2':2}

src/p/y/pycogent-HEAD/tests/test_parse/test_meme.py   pycogent(Download)
import string
import re
from cogent.motif.util import Motif
from cogent.core.moltype import DNA
from cogent.parse.record import DelimitedSplitter

src/p/y/pycogent-HEAD/tests/test_parse/test_gibbs.py   pycogent(Download)
import string
import re
from cogent.motif.util import Motif,Module
from cogent.core.moltype import DNA,RNA,PROTEIN
from cogent.parse.record import DelimitedSplitter

  1 | 2  Next