def main():
parser = parseArguments()
args = parser.parse_args()
if args.logLevel == 'DEBUG':
logger = clashchimeras.log.debug_logger('root')
elif args.logLevel == 'WARNING':
logger = clashchimeras.log.warning_logger('root')
elif args.logLevel == 'ERROR':
logger = clashchimeras.log.error_logger('root')
else:
logger = clashchimeras.log.info_logger('root')
argCheck = Arguments(args)
argCheck.validateAlign()
if args.run == 'bowtie2':
b = Bowtie(args=args)
b.run(output='smallRNA')
s = SAM(fileName=b.outputSam)
filteredFasta = s.filterPotentialChimeras(target=b.outputSam)
b.run(output='targetRNA', filtered=filteredFasta)
if args.run == 'tophat':
t = Tophat(args=args)
t.run()
def parseArguments():
requiredArgs = getRequiredArgs()
bowtieArgs = getBowtie2Args()
tophatArgs = getTophatArgs()
optionalArgs = getOptionalArgs()
outputArgs = getOutputArgs()
parser = argparse.ArgumentParser(
parents=[requiredArgs, bowtieArgs, tophatArgs,
outputArgs, optionalArgs],
formatter_class=CustomFormatter,
description='Given a fastq file, this script executes '
'bowtie2 and tophat aligners to generate alignment files '
'necessary for detecting chimeras in the reads',
usage='\n %(prog)s -i input.fastq -si '
'/path/to/smallRNA_index -ti /path/to/targetRNA_index -o '
'output -r bowtie2 \n %(prog)s -i input.fastq -gi '
'/path/to/genome_index -tri /path/to/transcriptome_index '
'-o output -r tophat \n \n \n '
'To see detailed help, please run \n %(prog)s -h',
add_help=True)
return parser
args = parser.parse_args()
if args.logLevel == 'DEBUG':
logger = clashchimeras.log.debug_logger('root')
elif args.logLevel == 'WARNING':
logger = clashchimeras.log.warning_logger('root')
elif args.logLevel == 'ERROR':
logger = clashchimeras.log.error_logger('root')
else:
logger = clashchimeras.log.info_logger('root')
argCheck = Arguments(args, type='align')
argCheck.validateAlign()
return args
