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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 
 
    except KeyError:
        score_matrix = make_dna_scoring_dict(\
         match=1,transition=-1,transversion=-1)
 
    return local_pairwise(s1,s2,score_matrix,gap_open,gap_extend)

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, \
    except KeyError:
        score_matrix = make_dna_scoring_dict(\
         match=1,transition=-1,transversion=-1)
 
    return global_pairwise(s1,s2,score_matrix,gap_open,gap_extend)

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
    except KeyError:
        score_matrix = make_dna_scoring_dict(
            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 _aligned_both_ways(self, seq1, seq2, **kw):
        S = make_dna_scoring_dict(10, -1, -8)
        a1 = classic_align_pairwise(seq1, seq2, S, 10, 2, **kw)
        a2 = classic_align_pairwise(seq2, seq1, S, 10, 2, **kw)
        return [a1, a2]
    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)
    def test_local_tiebreak(self):
        """Should pick the first best-equal hit rather than the last one"""
        # so that the Pyrex and Python versions give the same result.
        score_matrix = make_dna_scoring_dict(match=1, transition=-1, 
                transversion=-1)

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 _aligned_both_ways(self, seq1, seq2, **kw):
        S = make_dna_scoring_dict(10, -1, -8)
        a1 = classic_align_pairwise(seq1, seq2, S, 10, 2, **kw)
        a2 = classic_align_pairwise(seq2, seq1, S, 10, 2, **kw)
        return [a1, a2]
    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)
    def test_local_tiebreak(self):
        """Should pick the first best-equal hit rather than the last one"""
        # so that the Pyrex and Python versions give the same result.
        score_matrix = make_dna_scoring_dict(match=1, transition=-1, 
                transversion=-1)

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]

src/c/o/cogent-1.5.3/tests/benchmark_aligning.py   cogent(Download)
import time
from cogent import DNA
from cogent.align.align import classic_align_pairwise, make_dna_scoring_dict
 
__author__ = "Peter Maxwell"
def test(r=1, **kw):   
    S = make_dna_scoring_dict(10, -1, -8)
 
    seq2 = DNA.makeSequence('AAAATGCTTA' * r)
    seq1 = DNA.makeSequence('AATTTTGCTG' * r)

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]

src/p/y/pycogent-HEAD/tests/benchmark_aligning.py   pycogent(Download)
import time
from cogent import DNA
from cogent.align.align import classic_align_pairwise, make_dna_scoring_dict
 
__author__ = "Peter Maxwell"
def test(r=1, **kw):   
    S = make_dna_scoring_dict(10, -1, -8)
 
    seq2 = DNA.makeSequence('AAAATGCTTA' * r)
    seq1 = DNA.makeSequence('AATTTTGCTG' * r)