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)
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)