def prepare_bam(bam: str) -> Tuple[Tuple, str]:
"""Checks for file extension, and returns tuple of mapped refs
Args:
bam (str): Path to bam file
Returns:
Tuple: Tuple of mapped references
str: bam opening mode
"""
mode = check_extension(bam)
alf = AlignmentFile(bam, mode)
if not alf.has_index():
print(f"BAM file {bam} has no index. Sort BAM file and provide index "
"before running pydamage.")
sys.exit(1)
present_refs = set()
for ref_stat in alf.get_index_statistics():
refname = ref_stat[0]
nb_mapped_reads = ref_stat[1]
if nb_mapped_reads > 0:
present_refs.add(refname)
alf.close()
return tuple(present_refs), mode
def test_set_meta_presorted():
b = Bam()
with get_dataset('1.bam') as dataset:
b.set_meta(dataset=dataset)
assert dataset.metadata.sort_order == "coordinate"
bam_file = AlignmentFile(
dataset.file_name,
mode="rb",
index_filename=dataset.metadata.bam_index.file_name)
assert bam_file.has_index() is True
def main():
args = parse_args()
with args.bam_file:
bam_reader = AlignmentFile(args.bam_file)
if not bam_reader.has_index():
print('Adding index...')
index_args = ['samtools', 'index', args.bam_file.name]
run(index_args, check=True)
args.bam_file.seek(0) # Go back to start of header.
bam_reader = AlignmentFile(args.bam_file)
bam_reader.check_index()
x = bam_reader.parse_region(region=args.target_region)
sequences = sorted(bam_reader.fetch(region=args.target_region),
key=attrgetter('qname'))
print(len(sequences))
for seq in sequences:
print(seq.qname)
