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src/c/o/cogent-1.5.3/cogent/__init__.py   cogent(Download)
from cogent.parse.tree_xml import parse_string as tree_xml_parse_string
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
                label_to_name=label_to_name, **constructor_kw)
    else:   #generic case: return SequenceCollection
        return SequenceCollection(data, MolType=moltype, Name=name,
            label_to_name=label_to_name, **constructor_kw)
 

src/p/y/pycogent-HEAD/cogent/__init__.py   pycogent(Download)
from cogent.parse.tree_xml import parse_string as tree_xml_parse_string
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
                label_to_name=label_to_name, **constructor_kw)
    else:   #generic case: return SequenceCollection
        return SequenceCollection(data, MolType=moltype, Name=name,
            label_to_name=label_to_name, **constructor_kw)
 

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
                continue
            seqs.append((seq.Name, seq))
        return SequenceCollection(data=seqs, MolType=DNA)
 
    def getSeqLengths(self):

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
                continue
            seqs.append((seq.Name, seq))
        return SequenceCollection(data=seqs, MolType=DNA)
 
    def getSeqLengths(self):

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
 
    # Setup mapping. Clustalw clips identifiers. We will need to remap them.
    seq_collection = SequenceCollection(aln)
    int_map, int_keys = seq_collection.getIntMap()
    int_map = SequenceCollection(int_map)
 
    # Setup mapping. Clustalw clips identifiers. We will need to remap them.
    seq_collection = SequenceCollection(aln)
    int_map, int_keys = seq_collection.getIntMap()
    int_map = SequenceCollection(int_map)

src/c/o/cogent-1.5.3/cogent/app/muscle_v38.py   cogent(Download)
    get_tmp_filename, guess_input_handler
from random import choice
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.parse.tree import DndParser
from cogent.core.tree import PhyloNode
        params = {}
    #create SequenceCollection object from seqs
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    app.Parameters['-seqtype'].on(moltype.label)
 
    seq_collection = SequenceCollection(aln, MolType=moltype)
 
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)

src/c/o/cogent-1.5.3/cogent/app/muscle.py   cogent(Download)
    get_tmp_filename, guess_input_handler
from random import choice
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.parse.tree import DndParser
from cogent.core.tree import PhyloNode
        params = {}
    #create SequenceCollection object from seqs
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    app.Parameters['-seqtype'].on(moltype.label)
 
    seq_collection = SequenceCollection(aln, MolType=moltype)
 
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)

src/p/y/pycogent-HEAD/cogent/app/clustalw.py   pycogent(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
 
    # Setup mapping. Clustalw clips identifiers. We will need to remap them.
    seq_collection = SequenceCollection(aln)
    int_map, int_keys = seq_collection.getIntMap()
    int_map = SequenceCollection(int_map)
 
    # Setup mapping. Clustalw clips identifiers. We will need to remap them.
    seq_collection = SequenceCollection(aln)
    int_map, int_keys = seq_collection.getIntMap()
    int_map = SequenceCollection(int_map)

src/p/y/pycogent-HEAD/cogent/app/muscle_v38.py   pycogent(Download)
    get_tmp_filename, guess_input_handler
from random import choice
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.parse.tree import DndParser
from cogent.core.tree import PhyloNode
        params = {}
    #create SequenceCollection object from seqs
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    app.Parameters['-seqtype'].on(moltype.label)
 
    seq_collection = SequenceCollection(aln, MolType=moltype)
 
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)

src/p/y/pycogent-HEAD/cogent/app/muscle.py   pycogent(Download)
    get_tmp_filename, guess_input_handler
from random import choice
from cogent.core.alignment import SequenceCollection, Alignment
from cogent.parse.tree import DndParser
from cogent.core.tree import PhyloNode
        params = {}
    #create SequenceCollection object from seqs
    seq_collection = SequenceCollection(seqs,MolType=moltype)
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)
    app.Parameters['-seqtype'].on(moltype.label)
 
    seq_collection = SequenceCollection(aln, MolType=moltype)
 
    #Create mapping between abbreviated IDs and full IDs
    int_map, int_keys = seq_collection.getIntMap()
    #Create SequenceCollection from int_map.
    int_map = SequenceCollection(int_map,MolType=moltype)

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