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src/p/y/pynast-1.2.2/pynast/util.py   pynast(Download)
from cogent.util.misc import remove_files
from cogent.core.alignment import SequenceCollection, DenseAlignment
from cogent.align.align import make_dna_scoring_dict, global_pairwise
from cogent.app.blast import blastn
from cogent.app.formatdb import build_blast_db_from_seqs, \
         match=1,transition=-1,transversion=-1)
 
    return global_pairwise(s1,s2,score_matrix,gap_open,gap_extend)
 
def blast_align_unaligned_seqs(seqs,

src/c/o/cogent-1.5.3/tests/test_align/test_align.py   cogent(Download)
#!/usr/bin/env python
 
from cogent import DNA, LoadSeqs
from cogent.align.align import classic_align_pairwise, make_dna_scoring_dict,\
        local_pairwise, global_pairwise
        aln, score = local_pairwise(seq1, seq2, S, 10, 2, return_score=True)
        self.assertTrue(score > 100)
        aln, score = global_pairwise(seq1, seq2, S, 10, 2, return_score=True)
        self.assertTrue(score > 100)
 

src/p/y/pycogent-HEAD/tests/test_align/test_align.py   pycogent(Download)
#!/usr/bin/env python
 
from cogent import DNA, LoadSeqs
from cogent.align.align import classic_align_pairwise, make_dna_scoring_dict,\
        local_pairwise, global_pairwise
        aln, score = local_pairwise(seq1, seq2, S, 10, 2, return_score=True)
        self.assertTrue(score > 100)
        aln, score = global_pairwise(seq1, seq2, S, 10, 2, return_score=True)
        self.assertTrue(score > 100)
 

src/c/o/cogent-1.5.3/tests/test_draw.py   cogent(Download)
def makeSampleAlignment():
    # must be an esier way to make an alignment of annotated sequences!
    from cogent.align.align import global_pairwise, make_dna_scoring_dict
    DNA = make_dna_scoring_dict(10, -8, -8)
    seq1 = makeSampleSequence()[:-2]
    seq2.Name = 'FAKE02'
    names = (seq1.getName(), seq2.getName())
    align = global_pairwise(seq1, seq2, DNA, 2, 1)
    align.addAnnotation(annotation.Variable, 'redline', 'align', [((0,15),1),((15,30),2),((30,45),3)])
    align.addAnnotation(annotation.Variable, 'blueline', 'align', [((0,15),1.5),((15,30),2.5),((30,45),3.5)])

src/p/y/pycogent-HEAD/tests/test_draw.py   pycogent(Download)
def makeSampleAlignment():
    # must be an esier way to make an alignment of annotated sequences!
    from cogent.align.align import global_pairwise, make_dna_scoring_dict
    DNA = make_dna_scoring_dict(10, -8, -8)
    seq1 = makeSampleSequence()[:-2]
    seq2.Name = 'FAKE02'
    names = (seq1.getName(), seq2.getName())
    align = global_pairwise(seq1, seq2, DNA, 2, 1)
    align.addAnnotation(annotation.Variable, 'redline', 'align', [((0,15),1),((15,30),2),((30,45),3)])
    align.addAnnotation(annotation.Variable, 'blueline', 'align', [((0,15),1.5),((15,30),2.5),((30,45),3.5)])