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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, \
                else:
                    #Create a new module and add to dict
                    self.ModuleDict[word]=Module({(key,i):curr_instance},\
                        MolType=self.MolType)
        #Get list of counts

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, \
                else:
                    #Create a new module and add to dict
                    self.ModuleDict[word]=Module({(key,i):curr_instance},\
                        MolType=self.MolType)
        #Get list of counts

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
        meme_module[(seqId,start)] = mod_instance
 
    meme_module = Module(meme_module, MolType=alphabet)
    #Get Multilevel Consensus Sequence
    meme_module.ConsensusSequence = getConsensusSequence(module_data[1])

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
        meme_module[(seqId,start)] = mod_instance
 
    meme_module = Module(meme_module, MolType=alphabet)
    #Get Multilevel Consensus Sequence
    meme_module.ConsensusSequence = getConsensusSequence(module_data[1])

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
 
        gibbs_module[(seq_id,start)]=mod_instance
    gibbs_mod = Module(gibbs_module,MolType=alphabet)
    gibbs_mod.Pvalue = motif_p
    gibbs_mod.ID = motif_id + module_keys[0]

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
 
        gibbs_module[(seq_id,start)]=mod_instance
    gibbs_mod = Module(gibbs_module,MolType=alphabet)
    gibbs_mod.Pvalue = motif_p
    gibbs_mod.ID = motif_id + module_keys[0]

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,\
                                                       self.Evalues[i]))
        self.module_no_template = Module(
            {
                (self.modules_no_e[0].Location.SeqId,
                 self.modules_no_e[0].Location.Start):self.modules_no_e[0],
 
        self.module_with_template = Module(
            {
                (self.modules_no_e[0].Location.SeqId,
                 self.modules_no_e[0].Location.Start):self.modules_no_e[0],
    def test_init(self):
        """Init should properly initialize Module object."""
        module = Module(data={(self.modules_no_e[0].Location.SeqId,
                           self.modules_no_e[0].Location.Start): \
                          self.modules_no_e[0]})
                                            self.Pvalues,
                                            self.Evalues):
            modules.append(Module({(instance.Location.SeqId,
                                   instance.Location.Start):instance},
                                  Pvalue=pvalue,

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,\
                                                       self.Evalues[i]))
        self.module_no_template = Module(
            {
                (self.modules_no_e[0].Location.SeqId,
                 self.modules_no_e[0].Location.Start):self.modules_no_e[0],
 
        self.module_with_template = Module(
            {
                (self.modules_no_e[0].Location.SeqId,
                 self.modules_no_e[0].Location.Start):self.modules_no_e[0],
    def test_init(self):
        """Init should properly initialize Module object."""
        module = Module(data={(self.modules_no_e[0].Location.SeqId,
                           self.modules_no_e[0].Location.Start): \
                          self.modules_no_e[0]})
                                            self.Pvalues,
                                            self.Evalues):
            modules.append(Module({(instance.Location.SeqId,
                                   instance.Location.Start):instance},
                                  Pvalue=pvalue,

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

src/c/o/cogent-1.5.3/tests/test_parse/test_gibbs.py   cogent(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