test_CollapsingUtils.py 文件源码

def test_concatenate_sam(self):
        """Test concatenate_sam(in_sam_files, out_sam)"""
        in_sam_files = [op.join(_SIV_DIR_, f)
                        for f in ["chunk0.sam", "chunk1.sam"]]
        out_sam = op.join(_OUT_DIR_, 'test concatenated.sam')
        expected_sam = op.join(_SIV_DIR_, "sorted-gmap-output.sam")
        concatenate_sam(in_sam_files, out_sam)

        self.assertTrue(op.exists(out_sam))
        self.assertTrue(op.exists(expected_sam))

        #self.assertTrue(filecmp.cmp(out_sam, expected_sam))
        out = [l for l in open(out_sam, 'r') if not l.startswith('@PG')]
        exp = [l for l in open(expected_sam, 'r') if not l.startswith('@PG')]
        # test everything other than @PG are identical
        self.assertEqual(out, exp)

        # chunk01.sam and chunk02.sam has identical PG ID in their SAM headers
        # test concatenated @PG IDs are not conflicting
        pg_ids = [x[3:] for pg in [l for l in open(out_sam, 'r') if l.startswith('@PG')]
                  for x in pg.split('\t') if x.startswith('ID:')]
        self.assertEqual(len(pg_ids), len(set(pg_ids)))
        self.assertEqual(len(pg_ids), 2)