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
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