def test_calmd_bam(self):
ref_fpath = os.path.join(TEST_DATA_DIR, 'CUUC00007_TC01.fasta')
bam_fpath = os.path.join(TEST_DATA_DIR, 'sample.bam')
orig_qual = pysam.Samfile(bam_fpath).next().qual
out_bam = NamedTemporaryFile()
calmd_bam(bam_fpath, ref_fpath, out_bam.name)
samfile = pysam.Samfile(out_bam.name)
calmd_qual = alignment = samfile.next().qual
assert orig_qual != calmd_qual
assert calmd_qual == 'HHHHHHBHGGH!!!!!!!!!!!!!!!!!!!!!!!!!!!'
def test_calmd_no_out(self):
ref_fpath = os.path.join(TEST_DATA_DIR, 'CUUC00007_TC01.fasta')
bam_fpath = os.path.join(TEST_DATA_DIR, 'sample.bam')
copied_fpath = os.path.join(TEST_DATA_DIR, 'sample_copy.bam')
try:
shutil.copy(bam_fpath, copied_fpath)
orig_stats = os.stat(copied_fpath)
calmd_bam(copied_fpath, ref_fpath)
calmd_stats = os.stat(copied_fpath)
assert calmd_stats != orig_stats
finally:
if os.path.exists(copied_fpath):
os.remove(copied_fpath)
def test_calmd_no_out(self):
ref_fpath = os.path.join(TEST_DATA_DIR, 'CUUC00007_TC01.fasta')
bam_fpath = os.path.join(TEST_DATA_DIR, 'sample.bam')
copied_fpath = os.path.join(TEST_DATA_DIR, 'sample_copy.bam')
try:
shutil.copy(bam_fpath, copied_fpath)
orig_stats = os.stat(copied_fpath)
calmd_bam(copied_fpath, ref_fpath)
calmd_stats = os.stat(copied_fpath)
assert calmd_stats != orig_stats
finally:
if os.path.exists(copied_fpath):
os.remove(copied_fpath)
def test_calmd_bam(self):
ref_fpath = os.path.join(TEST_DATA_DIR, "CUUC00007_TC01.fasta")
bam_fpath = os.path.join(TEST_DATA_DIR, "sample.bam")
orig_qual = AlignmentFile(bam_fpath).next().qual
try:
out_bam = NamedTemporaryFile()
calmd_bam(bam_fpath, ref_fpath, out_bam.name)
samfile = AlignmentFile(out_bam.name)
calmd_qual = samfile.next().qual
assert orig_qual != calmd_qual
assert calmd_qual == "HHHHHHBHGGH!!!!!!!!!!!!!!!!!!!!!!!!!!!"
finally:
if os.path.exists(out_bam.name):
out_bam.close()
def test_calmd_bam(self):
ref_fpath = os.path.join(TEST_DATA_DIR, 'CUUC00007_TC01.fasta')
bam_fpath = os.path.join(TEST_DATA_DIR, 'sample.bam')
orig_qual = AlignmentFile(bam_fpath).next().qual
try:
out_bam = NamedTemporaryFile()
calmd_bam(bam_fpath, ref_fpath, out_bam.name)
samfile = AlignmentFile(out_bam.name)
calmd_qual = samfile.next().qual
assert orig_qual != calmd_qual
assert calmd_qual == 'HHHHHHBHGGH!!!!!!!!!!!!!!!!!!!!!!!!!!!'
finally:
if os.path.exists(out_bam.name):
out_bam.close()