Python filter_read_pair Examples

Example #1

File: filter_mapped_reads.py Project: iosonofabio/hivwholeseq

    def test(self):
        '''Test match only pairs'''
        pair_orig = deepcopy(self.pair)

        # Call the function
        pair_type = filter_read_pair(self.pair, self.ref, match_len_min=3)

        self.assertEqual(pair_type, 'good')
        self.assertEqual(self.pair, pair_orig)

Example #2

File: filter_mapped_reads.py Project: 5l1v3r1/hivwholeseq

    def test(self):
        '''Test match only pairs'''
        pair_orig = deepcopy(self.pair)

        # Call the function
        pair_type = filter_read_pair(self.pair, self.ref, match_len_min=3)

        self.assertEqual(pair_type, 'good')
        self.assertEqual(self.pair, pair_orig)

Example #3

File: filter_mapped_reads.py Project: iosonofabio/hivwholeseq

    def test(self):
        '''Test match only pairs'''
        pair = deepcopy(self.pair)
        pair[0].seq = pair[0].seq[7:]
        pair[0].qual = pair[0].qual[7:]
        pair[0].pos = 1
        pair[0].cigar = [(0, len(pair[0].seq))]
        pair[1].mpos = 1
        fix_pair(pair)

        # Call the function
        pair_type = filter_read_pair(self.pair, self.ref,
                                     trim_bad_cigars=1,
                                     match_len_min=3)

        self.assertEqual(pair_type, 'good')
        self.assertEqual(self.pair, pair)

Example #4

File: filter_mapped_reads.py Project: 5l1v3r1/hivwholeseq

    def test(self):
        '''Test match only pairs'''
        pair = deepcopy(self.pair)
        pair[0].seq = pair[0].seq[7:]
        pair[0].qual = pair[0].qual[7:]
        pair[0].pos = 1
        pair[0].cigar = [(0, len(pair[0].seq))]
        pair[1].mpos = 1
        fix_pair(pair)

        # Call the function
        pair_type = filter_read_pair(self.pair,
                                     self.ref,
                                     trim_bad_cigars=1,
                                     match_len_min=3)

        self.assertEqual(pair_type, 'good')
        self.assertEqual(self.pair, pair)