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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_CigarParser(self):
        """test without slice"""
        aln = CigarParser(self.seqs, self.cigars)
        assert aln == self.aln
        # test slice
            i += 1
 
            cmp_aln = CigarParser(self.seqs, self.cigars, sliced = True,
                                  ref_seqname = "FAKE01", start = start, end = end)
            assert cmp_aln == slice_aln 

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_CigarParser(self):
        """test without slice"""
        aln = CigarParser(self.seqs, self.cigars)
        assert aln == self.aln
        # test slice
            i += 1
 
            cmp_aln = CigarParser(self.seqs, self.cigars, sliced = True,
                                  ref_seqname = "FAKE01", start = start, end = end)
            assert cmp_aln == slice_aln