Did I find the right examples for you? yes no      Crawl my project      Python Jobs

All Samples(10)  |  Call(8)  |  Derive(0)  |  Import(2)

src/c/o/cogent-1.5.3/cogent/db/ensembl/related_region.py   cogent(Download)
            relative_end = relative_start + len(ref_location)
 
        aln_map, aln_loc = cigar.slice_cigar(self.cigar_line, relative_start,
                                         relative_end, by_align = False)
 
        record = self._cached
        try:
            aln_map, aln_loc = cigar.slice_cigar(self.cigar_line,
                                            self.parent.CigarStart,
                                            self.parent.CigarEnd,

src/p/y/pycogent-HEAD/cogent/db/ensembl/related_region.py   pycogent(Download)
            relative_end = relative_start + len(ref_location)
 
        aln_map, aln_loc = cigar.slice_cigar(self.cigar_line, relative_start,
                                         relative_end, by_align = False)
 
        record = self._cached
        try:
            aln_map, aln_loc = cigar.slice_cigar(self.cigar_line,
                                            self.parent.CigarStart,
                                            self.parent.CigarEnd,

src/c/o/cogent-1.5.3/tests/test_parse/test_cigar.py   cogent(Download)
#!/usr/bin/env python
import unittest, sys, os
from cogent import DNA, LoadSeqs
from cogent.parse.cigar import map_to_cigar, cigar_to_map, aligned_from_cigar, \
                                slice_cigar, CigarParser
    def test_slice_cigar(self):
        """test slicing cigars"""
        for start, end in self.slices:
            # test by_align = True
            map1, loc1 = slice_cigar(self.cigar_text, start, end)
 
            # test by_align = False
            map2, loc2 = slice_cigar(self.cigar_text, start, end, by_align = False)
            slicealn2 = self.seq[start:end].gappedByMap(map2)
            ori2 = self.aln_seq[loc2[0]:loc2[1]]

src/p/y/pycogent-HEAD/tests/test_parse/test_cigar.py   pycogent(Download)
#!/usr/bin/env python
import unittest, sys, os
from cogent import DNA, LoadSeqs
from cogent.parse.cigar import map_to_cigar, cigar_to_map, aligned_from_cigar, \
                                slice_cigar, CigarParser
    def test_slice_cigar(self):
        """test slicing cigars"""
        for start, end in self.slices:
            # test by_align = True
            map1, loc1 = slice_cigar(self.cigar_text, start, end)
 
            # test by_align = False
            map2, loc2 = slice_cigar(self.cigar_text, start, end, by_align = False)
            slicealn2 = self.seq[start:end].gappedByMap(map2)
            ori2 = self.aln_seq[loc2[0]:loc2[1]]