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globalms(sequenceA, sequenceB, match, mismatch, open, extend) -> alignments

match is the score to given to identical characters.  mismatch is
the score given to non-identical ones.

open and extend are the gap penalties when a gap is opened and
extended.  They should be negative.

alignments is a list of tuples (seqA, seqB, score, begin, end).
seqA and seqB are strings showing the alignment between the(more...)

src/b/c/bcbb-HEAD/nextgen/scripts/barcode_sort_trim.py   bcbb(Download)
            else:
                gapopen_penalty = -9.0
            aligns = pairwise2.align.globalms(bc_seq, test_seq,
                    5.0, -4.0, gapopen_penalty, -0.5, one_alignment_only=True)
            (abc_seq, atest_seq) = aligns[0][:2] if len(aligns) == 1 else ("", "")

src/s/e/seqmagick-0.5.0/seqmagick/subcommands/primer_trim.py   seqmagick(Download)
        """
        seq_aln, primer_aln, score, start, end = \
                pairwise2.align.globalms(str(sequence), str(self.primer),
                        self.match, self.difference, self.gap_open,
                        self.gap_extend, one_alignment_only=True)[0]

src/s/e/seqmagick-HEAD/seqmagick/subcommands/primer_trim.py   seqmagick(Download)
        """
        seq_aln, primer_aln, score, start, end = \
                pairwise2.align.globalms(str(sequence).upper(), str(self.primer).upper(),
                        self.match, self.difference, self.gap_open,
                        self.gap_extend, one_alignment_only=True)[0]

src/b/c/bcbio-nextgen-0.7.8/scripts/barcode_sort_trim.py   bcbio-nextgen(Download)
            else:
                gapopen_penalty = -9.0
            aligns = pairwise2.align.globalms(bc_seq, test_seq,
                    5.0, -4.0, gapopen_penalty, -0.5, one_alignment_only=True)
            (abc_seq, atest_seq) = aligns[0][:2] if len(aligns) == 1 else ("", "")

src/p/y/pytools-HEAD/seqtools.py   pytools(Download)
    return reduce(lambda cumul,garbage:cumul+choice('ACGT'),xrange(n),'')
 
global_align = lambda seq1,seq2: pairwise2.align.globalms(seq1,seq2,0.5,-0.75,-2.,-1.5,one_alignment_only=True)[0]
 
def percent_id(seq1,seq2):

src/c/o/ContactVis-0.1.5/contactvis/plot_contact_map.py   ContactVis(Download)
        atom_seq = parse_pdb.get_atom_seq(open(pdb_filename, 'r'), chain)
 
        align = pairwise2.align.globalms(atom_seq, seq, 2, -1, -0.5, -0.1)
 
        atom_seq_ali = align[-1][0]

src/b/i/biopython-1.63/Tests/test_pairwise2.py   biopython(Download)
    def test_match_score_open_penalty1(self):
        aligns = pairwise2.align.globalms("AA", "A", 2.0, -1, -0.1, 0)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_match_score_open_penalty2(self):
        aligns = pairwise2.align.globalms("GAA", "GA", 1.5, 0, -0.1, 0)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_match_score_open_penalty4(self):
        aligns = pairwise2.align.globalms("GCT", "GATA", 1, -2, -0.1, 0)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)

src/b/i/biopython-HEAD/Tests/test_pairwise2.py   biopython(Download)
    def test_match_score_open_penalty1(self):
        aligns = pairwise2.align.globalms("AA", "A", 2.0, -1, -0.1, 0)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_match_score_open_penalty2(self):
        aligns = pairwise2.align.globalms("GAA", "GA", 1.5, 0, -0.1, 0)
        self.assertEqual(len(aligns), 2)
        aligns.sort()
        seq1, seq2, score, begin, end = aligns[0]
    def test_match_score_open_penalty4(self):
        aligns = pairwise2.align.globalms("GCT", "GATA", 1, -2, -0.1, 0)
        self.assertEqual(len(aligns), 1)
        seq1, seq2, score, begin, end = aligns[0]
        alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)