def _check_input_bam_valid(args, log=None): #pylint: disable=unused-argument
try:
bamfile = samtools.alignment_file(args.input_bam, 'rb')
bamfile.close()
except ValueError:
raise utils.UsageError(("Specified input [{}] not a valid BAM. Review "
"inputs and try again.").format(args.input_bam))
def _check_input_bam_indexed(args, log=None): #pylint: disable=unused-argument
bamfile = samtools.alignment_file(args.input_bam, 'rb')
try:
bamfile.fetch()
except ValueError:
raise utils.UsageError(("Specified input [{}] is not indexed. Review "
"inputs and try again.").format(args.input_bam))
finally:
bamfile.close()
def _check_input_bam_not_empty(args, log=None): #pylint: disable=unused-argument
bamfile = samtools.alignment_file(args.input_bam, 'rb')
try:
next(bamfile.fetch())
except StopIteration:
msg = "Specified input [{}] is empty"
raise utils.UsageError(msg.format(args.input_bam))
finally:
bamfile.close()
def error(self, message):
'''Suppress default exit behavior'''
raise utils.UsageError(message)
def _check_input_bam_exists(args, log=None): #pylint: disable=unused-argument
if not os.path.exists(args.input_bam):
raise utils.UsageError(("Specified input [{}] does not exist. Review "
"inputs and try again.").format(args.input_bam))
def _log_force_or_raise(args, log, msg):
if args.force:
log.warning(msg + ' (**forcing**)')
else:
raise utils.UsageError(msg + ' Are you sure? (--force to proceed)')