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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
        location = Location(seqId, start, start + module_length)
        #Create ModuleInstance
        mod_instance = ModuleInstance(sequence,location,Pvalue)
 
        #Add ModuleInstance to Module

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
        location = Location(seqId, start, start + module_length)
        #Create ModuleInstance
        mod_instance = ModuleInstance(sequence,location,Pvalue)
 
        #Add ModuleInstance to Module

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

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

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, \
                location = Location(key,i,i+word_length)
                #Create a ModuleInstance
                curr_instance = ModuleInstance(word,location)
                #Check to see if pattern is already in dict
                if word in self.ModuleDict:
            curr_str = \
                self.Alignment[seq_id][module_start:module_end]
            curr_instance = ModuleInstance(curr_str,loc)
            module[k]=curr_instance
        return module

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, \
                location = Location(key,i,i+word_length)
                #Create a ModuleInstance
                curr_instance = ModuleInstance(word,location)
                #Check to see if pattern is already in dict
                if word in self.ModuleDict:
            curr_str = \
                self.Alignment[seq_id][module_start:module_end]
            curr_instance = ModuleInstance(curr_str,loc)
            module[k]=curr_instance
        return module

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.modules_no_e = []
        for i in xrange(7):
            self.modules_no_e.append(ModuleInstance(self.sequences[i],
                                                    self.locations[i],
                                                    self.Pvalues[i]))
        self.modules_p_and_e = []
        for i in xrange(7):
            self.modules_p_and_e.append(ModuleInstance(self.sequences[i],
                                                       self.Evalues[i]))
        self.modules_no_e_sorted = [
            ModuleInstance(self.sequences[2],self.locations[2],self.Pvalues[2]),
            ModuleInstance(self.sequences[1],self.locations[1],self.Pvalues[1]),
            ModuleInstance(self.sequences[6],self.locations[6],self.Pvalues[6]),

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.modules_no_e = []
        for i in xrange(7):
            self.modules_no_e.append(ModuleInstance(self.sequences[i],
                                                    self.locations[i],
                                                    self.Pvalues[i]))
        self.modules_p_and_e = []
        for i in xrange(7):
            self.modules_p_and_e.append(ModuleInstance(self.sequences[i],
                                                       self.Evalues[i]))
        self.modules_no_e_sorted = [
            ModuleInstance(self.sequences[2],self.locations[2],self.Pvalues[2]),
            ModuleInstance(self.sequences[1],self.locations[1],self.Pvalues[1]),
            ModuleInstance(self.sequences[6],self.locations[6],self.Pvalues[6]),