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src/b/i/biopython-1.63/Bio/Motif/Parsers/AlignAce.py   biopython(Download)
        elif len(line.split("\t"))==4:
            seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
            record.current_motif.add_instance(seq)
        elif "*" in line:
            record.current_motif.set_mask(line.strip("\n\c"))

src/b/i/biopython-HEAD/Bio/Motif/Parsers/AlignAce.py   biopython(Download)
        elif len(line.split("\t"))==4:
            seq = Seq(line.split("\t")[0], IUPAC.unambiguous_dna)
            record.current_motif.add_instance(seq)
        elif "*" in line:
            record.current_motif.set_mask(line.strip("\n\c"))

src/w/l/wLib-1.1.0/external/Motif/Parsers/AlignAce.py   wLib(Download)
        elif len(line.split("\t"))==4:
            seq = Seq(line.split("\t")[0],IUPAC.unambiguous_dna)
            record.current_motif.add_instance(seq)
        elif "*" in line:
            record.current_motif.set_mask(line.strip("\n\c"))

src/h/y/hy454-0.4.4/lib/hy454/_graph.py   hy454(Download)
    instances = [''.join(z).upper() for z in zip(*[alignment[:, i] for i in columns])]
    for instance in instances:
        motif.add_instance(Seq(instance, alph))
 
    # set laplace = True to include the backgrounds

src/r/n/rnaseqlib-HEAD/rnaseqlib/motif/motif_clustering.py   rnaseqlib(Download)
    for clustalw_seq in clustalw_input.get_all_seqs():
        curr_seq = bio_seq.Seq(str(clustalw_seq.seq), IUPAC.unambiguous_dna)
        motif_obj.add_instance(curr_seq)
    # Compute PWM
    pwm = motif_obj.pwm()

src/b/i/biopython-1.63/Bio/Motif/Parsers/MEME.py   biopython(Download)
        if self.name:
            inst._motifname(self.name)
        self.add_instance(inst)
 
    def _evalue (self, evalue):

src/b/i/biopython-HEAD/Bio/Motif/Parsers/MEME.py   biopython(Download)
        if self.name:
            inst._motifname(self.name)
        self.add_instance(inst)
 
    def _evalue (self, evalue):

src/w/l/wLib-1.1.0/external/Motif/Parsers/MEME.py   wLib(Download)
        if self.name:
            inst._motifname(self.name)
        self.add_instance(inst)
 
    def _evalue (self, evalue):

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

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