test_bam_stats.py 文件源码

def test_fragment_stats(self):
        """Test the gathering of fragment statistics."""
        top = path.dirname(__file__)
        bam = path.join(top, "data/test_bam_stats/stat_test.bam")
        ref = path.join(top, "data/test_bam_stats/stat_ref.fas")
        references = SeqIO.index(ref, format='fasta')
        chrom_lengths = {name: len(so) for name, so in six.iteritems(references)}
        res = stats.frag_coverage(bam, chrom_lengths, region=None, min_aqual=0, verbose=False)

        self.maxDiff = None
        target = [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
                  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
                  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
                  0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
        self.assertEqual(list(res['frags_fwd']['seq_0']), target)