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src/q/i/qiime-1.8.0/qiime/split_libraries.py   qiime(Download)
from cogent.core.moltype import IUPAC_DNA_ambiguities
from cogent import DNA, LoadSeqs
from cogent.align.align import make_dna_scoring_dict, local_pairwise
from cogent.util.misc import remove_files 
 
         match=1,transition=-1,transversion=-1)
 
    return local_pairwise(s1,s2,score_matrix,gap_open,gap_extend)
 
def local_align_primer_seq(primer,sequence,sw_scorer=equality_scorer_ambigs):

src/q/i/qiime-HEAD/qiime/split_libraries.py   qiime(Download)
from cogent import DNA as DNA_cogent, LoadSeqs
 
from cogent.align.align import make_dna_scoring_dict, local_pairwise
from skbio.util.misc import remove_files
from skbio.core.sequence import DNASequence
            match=1, transition=-1, transversion=-1)
 
    return local_pairwise(s1, s2, score_matrix, gap_open, gap_extend)
 
 

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
    def test_pairwise_returns_score(self):
        """exercise pairwise local/global returns alignment score"""
        S = make_dna_scoring_dict(10, -1, -8)
        aln, score = local_pairwise(seq1, seq2, S, 10, 2, return_score=True)
        self.assertTrue(score > 100)
        pattern = DNA.makeSequence('cwc', Name='pattern')
        two_hit = DNA.makeSequence( 'cactc', Name= 'target')
        aln = local_pairwise(pattern, two_hit, score_matrix, 5, 2)
        hit = aln.NamedSeqs['target']
        self.assertEqual(str(hit).lower(), 'cac')

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
    def test_pairwise_returns_score(self):
        """exercise pairwise local/global returns alignment score"""
        S = make_dna_scoring_dict(10, -1, -8)
        aln, score = local_pairwise(seq1, seq2, S, 10, 2, return_score=True)
        self.assertTrue(score > 100)
        pattern = DNA.makeSequence('cwc', Name='pattern')
        two_hit = DNA.makeSequence( 'cactc', Name= 'target')
        aln = local_pairwise(pattern, two_hit, score_matrix, 5, 2)
        hit = aln.NamedSeqs['target']
        self.assertEqual(str(hit).lower(), 'cac')