示例#1
0
 def test_batch(self):
     """The 'batch' command."""
     target_bed = "formats/my-targets.bed"
     fasta = "formats/chrM-Y-trunc.hg19.fa"
     bam = "formats/na12878-chrM-Y-trunc.bam"
     annot = "formats/my-refflat.bed"
     # Build a single-sample WGS reference
     ref_fname, tgt_bed_fname, _ = batch.batch_make_reference(
         [bam], None, None, True, fasta, annot, True, 500, None, None, None,
         None, 'build', 1, False, "wgs")
     self.assertEqual(ref_fname, 'build/reference.cnn')
     refarr = cnvlib.read(ref_fname, 'bed')
     tgt_regions = tabio.read(tgt_bed_fname, 'bed')
     self.assertEqual(len(refarr), len(tgt_regions))
     # Build a single-sample hybrid-capture reference
     ref_fname, tgt_bed_fname, anti_bed_fname = batch.batch_make_reference(
         [bam], target_bed, None, True, fasta, None, True, 10, None, 1000,
         100, None, 'build', 1, False, "hybrid")
     self.assertEqual(ref_fname, 'build/reference.cnn')
     refarr = cnvlib.read(ref_fname, 'bed')
     tgt_regions = tabio.read(tgt_bed_fname, 'bed')
     anti_regions = tabio.read(anti_bed_fname, 'bed')
     self.assertEqual(len(refarr), len(tgt_regions) + len(anti_regions))
     # Run the same sample
     batch.batch_run_sample(bam, tgt_bed_fname, anti_bed_fname, ref_fname,
                            'build', True, True, True, None, False, False,
                            "hybrid", 1)
     cns = cnvlib.read("build/na12878-chrM-Y-trunc.cns")
     self.assertGreater(len(cns), 0)
示例#2
0
 def test_batch(self):
     """The 'batch' command."""
     target_bed = "formats/my-targets.bed"
     fasta = "formats/chrM-Y-trunc.hg19.fa"
     bam = "formats/na12878-chrM-Y-trunc.bam"
     annot = "formats/my-refflat.bed"
     # Build a single-sample WGS reference
     ref_fname, tgt_bed_fname, _ = batch.batch_make_reference(
         [bam], None, None, True, fasta, annot, True, 500, None, None,
         None, None, 'build', 1, False, "wgs")
     self.assertEqual(ref_fname, 'build/reference.cnn')
     refarr = cnvlib.read(ref_fname, 'bed')
     tgt_regions = tabio.read(tgt_bed_fname, 'bed')
     self.assertEqual(len(refarr), len(tgt_regions))
     # Build a single-sample hybrid-capture reference
     ref_fname, tgt_bed_fname, anti_bed_fname = batch.batch_make_reference(
         [bam], target_bed, None, True, fasta, None, True, 10, None, 1000,
         100, None, 'build', 1, False, "hybrid")
     self.assertEqual(ref_fname, 'build/reference.cnn')
     refarr = cnvlib.read(ref_fname, 'bed')
     tgt_regions = tabio.read(tgt_bed_fname, 'bed')
     anti_regions = tabio.read(anti_bed_fname, 'bed')
     self.assertEqual(len(refarr), len(tgt_regions) + len(anti_regions))
     # Run the same sample
     batch.batch_run_sample(
         bam, tgt_bed_fname, anti_bed_fname, ref_fname, 'build', True,
         True, True, None, False, False, "hybrid", 1)
     cns =  cnvlib.read("build/na12878-chrM-Y-trunc.cns")
     self.assertGreater(len(cns), 0)