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src/c/o/cogent-1.5.3/cogent/__init__.py   cogent(Download)
from cogent.parse.newick import parse_string as newick_parse_string
from cogent.core.alignment import SequenceCollection
from cogent.core.alignment import Alignment
from cogent.parse.sequence import FromFilenameParser
from cogent.parse.structure import FromFilenameStructureParser
                label_to_name=label_to_name, **constructor_kw)
        else:   #was not callable, but wasn't False
            return Alignment(data=data, MolType=moltype, Name=name,
                label_to_name=label_to_name, **constructor_kw)
    else:   #generic case: return SequenceCollection

src/p/y/pycogent-HEAD/cogent/__init__.py   pycogent(Download)
from cogent.parse.newick import parse_string as newick_parse_string
from cogent.core.alignment import SequenceCollection
from cogent.core.alignment import Alignment
from cogent.parse.sequence import FromFilenameParser
from cogent.parse.structure import FromFilenameStructureParser
                label_to_name=label_to_name, **constructor_kw)
        else:   #was not callable, but wasn't False
            return Alignment(data=data, MolType=moltype, Name=name,
                label_to_name=label_to_name, **constructor_kw)
    else:   #generic case: return SequenceCollection

src/c/o/cogent-1.5.3/cogent/align/traceback.py   cogent(Download)
#!/usr/bin/env python
"""Conversion of dynamic program results ("arrays of arrows") into gap vectors,
gapped sequences or Cogent Alignment objects"""
 
from cogent.core.alignment import Alignment, Aligned
        gs = Aligned(amap*word_length, seq[start*word_length:end*word_length])
        aligneds.append((name, gs))
    return Alignment(MolType=None, data=aligneds)
 

src/p/y/pycogent-HEAD/cogent/align/traceback.py   pycogent(Download)
#!/usr/bin/env python
"""Conversion of dynamic program results ("arrays of arrows") into gap vectors,
gapped sequences or Cogent Alignment objects"""
 
from cogent.core.alignment import Alignment, Aligned
        gs = Aligned(amap*word_length, seq[start*word_length:end*word_length])
        aligneds.append((name, gs))
    return Alignment(MolType=None, data=aligneds)
 

src/c/o/cogent-1.5.3/cogent/db/ensembl/related_region.py   cogent(Download)
from pprint import pprint
import sqlalchemy as sql
 
from cogent import DNA
from cogent.core.alignment import SequenceCollection, Alignment, Aligned
            return None
 
        aln = Alignment(data=seqs, MolType=DNA)
 
        if self._rc:

src/p/y/pycogent-HEAD/cogent/db/ensembl/related_region.py   pycogent(Download)
from pprint import pprint
import sqlalchemy as sql
 
from cogent import DNA
from cogent.core.alignment import SequenceCollection, Alignment, Aligned
            return None
 
        aln = Alignment(data=seqs, MolType=DNA)
 
        if self._rc:

src/c/o/cogent-1.5.3/cogent/evolve/likelihood_function.py   cogent(Download)
#!/usr/bin/env python
 
import random, numpy
 
from cogent.core.alignment import Alignment
                seq.append(max(by_p)[1])
            seqs += [(edge, self.model.MolType.makeSequence("".join(seq)))]
        return Alignment(data = seqs, MolType = self.model.MolType)
 
    def getBinProbs(self, locus=None):
 
        return Alignment(
                data = simulated_sequences,
                MolType = self._model.MolType)
 

src/p/y/pycogent-HEAD/cogent/evolve/likelihood_function.py   pycogent(Download)
#!/usr/bin/env python
 
import random, numpy
 
from cogent.core.alignment import Alignment
                seq.append(max(by_p)[1])
            seqs += [(edge, self.model.MolType.makeSequence("".join(seq)))]
        return Alignment(data = seqs, MolType = self.model.MolType)
 
    def getBinProbs(self, locus=None):
 
        return Alignment(
                data = simulated_sequences,
                MolType = self._model.MolType)
 

src/c/o/cogent-1.5.3/cogent/app/clustalw.py   cogent(Download)
    MixedParameter, FilePath
from cogent.app.util import CommandLineApplication, ResultPath, remove
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.parse.tree import DndParser 
from cogent.parse.clustal import ClustalParser
        new_alignment[int_keys[k]]=v
    #Create an Alignment object from alignment dict
    new_alignment = Alignment(new_alignment,MolType=moltype)
    #Clean up
    res.cleanUp()
 
    #create Alignment object from aln
    aln = Alignment(aln,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    aln_int_map, aln_int_keys = aln.getIntMap(prefix='seqn_')
    #Create SequenceCollection from int_map.
    aln_int_map = Alignment(aln_int_map,MolType=moltype)
        new_alignment[seq_int_keys[k]]=v
    #Create an Alignment object from alignment dict
    new_alignment = Alignment(new_alignment,MolType=moltype)
    #Clean up
    res.cleanUp()

src/c/o/cogent-1.5.3/cogent/app/mafft.py   cogent(Download)
from cogent.parse.fasta import MinimalFastaParser
from cogent.core.moltype import DNA, RNA, PROTEIN
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.core.tree import PhyloNode
from cogent.parse.tree import DndParser
        new_alignment[int_keys[k]]=v
    #Create an Alignment object from alignment dict
    new_alignment = Alignment(new_alignment,MolType=moltype)
    #Clean up
    res.cleanUp()
 
    #create Alignment object from aln
    aln = Alignment(aln,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    aln_int_map, aln_int_keys = aln.getIntMap(prefix='seqn_')
    #Create SequenceCollection from int_map.
    aln_int_map = Alignment(aln_int_map,MolType=moltype)
        new_alignment[seq_int_keys[key]]=v
    #Create an Alignment object from alignment dict
    new_alignment = Alignment(new_alignment,MolType=moltype)
    #Clean up
    res.cleanUp()

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