def _make_autosomal_reference_file(out_file, data):
"""
for many organisms we don't know in bcbio what chromosomes are what, for now include
everything non-mitochondrial
"""
if utils.file_exists(out_file):
return out_file
nonmito = chromhacks.get_nonmitochondrial_chroms(data)
with file_transaction(out_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
for chrom in nonmito:
print(f"{chrom}", file=out_handle)
return out_file
def remove_mitochondrial_reads(bam_file, data):
mito = get_mitochondrial_chroms(data)
if not mito:
logger.info(
f"Mitochondrial chromosome not identified, skipping removal of "
"mitochondrial reads from {bam_file}.")
return bam_file
nonmito = get_nonmitochondrial_chroms(data)
mito_bam = os.path.splitext(bam_file)[0] + "-noMito.bam"
if utils.file_exists(mito_bam):
return mito_bam
samtools = config_utils.get_program("samtools", dd.get_config(data))
nonmito_flag = " ".join(nonmito)
num_cores = dd.get_num_cores(data)
with file_transaction(mito_bam) as tx_out_bam:
cmd = (f"{samtools} view -bh -@ {num_cores} {bam_file} {nonmito_flag} "
f"> {tx_out_bam}")
message = f"Removing mitochondrial reads on {','.join(mito)} from {bam_file}."
do.run(cmd, message)
return mito_bam