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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, \
                word = seq[i:i+word_length].tostring()
                #Create a location object
                location = Location(key,i,i+word_length)
                #Create a ModuleInstance
                curr_instance = ModuleInstance(word,location)
            seq_id, module_start = k
            module_end = module_start+module_len
            loc = Location(seq_id,module_start,module_end)
            curr_str = \
                self.Alignment[seq_id][module_start:module_end]

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, \
                word = seq[i:i+word_length].tostring()
                #Create a location object
                location = Location(key,i,i+word_length)
                #Create a ModuleInstance
                curr_instance = ModuleInstance(word,location)
            seq_id, module_start = k
            module_end = module_start+module_len
            loc = Location(seq_id,module_start,module_end)
            curr_str = \
                self.Alignment[seq_id][module_start:module_end]

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
        sequence = instance[4]
        #Create Location object for ModuleInstance
        location = Location(seqId, start, start + module_length)
        #Create ModuleInstance
        mod_instance = ModuleInstance(sequence,location,Pvalue)

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
        sequence = instance[4]
        #Create Location object for ModuleInstance
        location = Location(seqId, start, start + module_length)
        #Create ModuleInstance
        mod_instance = ModuleInstance(sequence,location,Pvalue)

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
 
        #Create Location object
        location = Location(seq_id, start, start + len(seq))
        #Create ModuleInstance
        mod_instance = ModuleInstance(seq,location,sig)

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
 
        #Create Location object
        location = Location(seq_id, start, start + len(seq))
        #Create ModuleInstance
        mod_instance = ModuleInstance(seq,location,sig)

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,\
    def setUp(self):
        """Setup for Location tests."""
        self.location_no_end = Location('seq1',1)
        self.locations = [
                        Location('seq1',1,5),
                        Location('seq2',3,54),
                        Location('seq1',5,3),

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,\
    def setUp(self):
        """Setup for Location tests."""
        self.location_no_end = Location('seq1',1)
        self.locations = [
                        Location('seq1',1,5),
                        Location('seq2',3,54),
                        Location('seq1',5,3),