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src/h/y/hy454-0.4.4/lib/hy454/_graph.py   hy454(Download)
from Bio.Alphabet.IUPAC import (ambiguous_dna, ambiguous_rna,
        extended_protein, unambiguous_dna, unambiguous_rna)
from Bio.Motif import Motif
from Bio.Seq import Seq
 
        raise RuntimeError("sequences with indeterminable alphabet provided")
 
    motif = Motif(alphabet=alph)
 
    instances = [''.join(z).upper() for z in zip(*[alignment[:, i] for i in columns])]

src/r/n/rnaseqlib-HEAD/rnaseqlib/motif/motif_clustering.py   rnaseqlib(Download)
        raise Exception, "CLUSTALW file %s does not exist" %(clustalw_fname)
    clustalw_input = align_io.read(clustalw_fname, "clustal")
    motif_obj = Motif.Motif(alphabet=IUPAC.unambiguous_dna)
    # Add sequences from CLUSTALW alignment to motif object
    for clustalw_seq in clustalw_input.get_all_seqs():

src/b/i/biopython-1.63/Bio/Motif/Parsers/MEME.py   biopython(Download)
from math import sqrt
import sys
from Bio.Motif import Motif
 
 
class MEMEMotif (Motif):
    """A subclass of Motif used in parsing MEME (and MAST) output.
 
    This sublcass defines functions and data specific to MEME motifs. 
    This includes the evalue for a motif and the PSSM of the motif.

src/b/i/biopython-1.63/Bio/Motif/Parsers/AlignAce.py   biopython(Download)
"""
 
from Bio.Motif import Motif
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq
            record.seq_dict=[]
        elif line[:5]=="Motif":
            record.current_motif = Motif()
            record.motifs.append(record.current_motif)
            record.current_motif.alphabet=IUPAC.unambiguous_dna

src/b/i/biopython-HEAD/Bio/Motif/Parsers/MEME.py   biopython(Download)
from math import sqrt
import sys
from Bio.Motif import Motif
 
 
class MEMEMotif (Motif):
    """A subclass of Motif used in parsing MEME (and MAST) output.
 
    This sublcass defines functions and data specific to MEME motifs. 
    This includes the evalue for a motif and the PSSM of the motif.

src/b/i/biopython-HEAD/Bio/Motif/Parsers/AlignAce.py   biopython(Download)
"""
 
from Bio.Motif import Motif
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq
            record.seq_dict=[]
        elif line[:5]=="Motif":
            record.current_motif = Motif()
            record.motifs.append(record.current_motif)
            record.current_motif.alphabet=IUPAC.unambiguous_dna

src/w/l/wLib-1.1.0/external/Motif/Parsers/MEME.py   wLib(Download)
from math import sqrt
import sys
from Bio.Motif import Motif
 
 
class MEMEMotif (Motif):
    """A subclass of Motif used in parsing MEME (and MAST) output.
 
    This sublcass defines functions and data specific to MEME motifs. 
    This includes the evalue for a motif and the PSSM of the motif.

src/w/l/wLib-1.1.0/external/Motif/Parsers/AlignAce.py   wLib(Download)
"""
 
from Bio.Motif import Motif
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq
            record.seq_dict=[]
        elif line[:5]=="Motif":
            record.current_motif = Motif()
            record.motifs.append(record.current_motif)
            record.current_motif.alphabet=IUPAC.unambiguous_dna

src/b/i/biopython-HEAD/Tests/test_Motif.py   biopython(Download)
        self.FAout = "Motif/fa.out"
        self.PFMout = "Motif/fa.out"
        self.m=Motif.Motif()
        self.m.add_instance(Seq("ATATA", self.m.alphabet))
 

src/b/i/biopython-1.63/Tests/test_Motif.py   biopython(Download)
        self.FAout = "Motif/fa.out"
        self.PFMout = "Motif/fa.out"
        self.m=Motif.Motif()
        self.m.add_instance(Seq("ATATA", self.m.alphabet))