def main(): #initialize the logging utils_logging.init_logging() #Setup options optparser = _prepare_optparser() (options, args) = optparser.parse_args() #verify options arg_pass = _verifyOption(options) utils_logging.change_log_stdout_to_log_stderr() if not arg_pass: logging.warning(optparser.get_usage()) logging.critical("Non valid arguments: exit") sys.exit(1) if options.mandatory_list_samples: mandatory_list_samples = options.mandatory_list_samples.split(',') else: mandatory_list_samples = None if options.list_samples: list_samples = options.list_samples.split(',') else: list_samples = None run_fine = vcf_to_simple_genotype( options.vcf_file, mandatory_list_samples, list_samples, options.nb_of_required_high_qual_genotype, options.print_all_genotype) if run_fine: logging.info('Run completed') else: logging.error('Run Failed') sys.exit(1)
def main(): #initialize the logging utils_logging.init_logging() #Setup options optparser=_prepare_optparser() (options,args) = optparser.parse_args() #verify options arg_pass=_verifyOption(options) if not arg_pass: logging.warning(optparser.get_usage()) logging.critical("Non valid arguments: exit") sys.exit(1) utils_logging.change_log_stdout_to_log_stderr() if options.print_commands: utils_logging.change_log_stdout_to_log_stderr() else: command_runner.set_command_to_run_localy() run_fine=run_BWA_Command(options.genome_file, options.fastq_file1, options.fastq_file2, options.output_dir, options.name,analysis_type=options.analysis, sort=options.sort, thread=options.thread, read_group=options.read_group, illumina=options.illumina) if run_fine: logging.info('Run completed') else: logging.error('Run Failed') sys.exit(1)
def main(): #initialize the logging utils_logging.init_logging() #Setup options optparser = _prepare_optparser() (options, args) = optparser.parse_args() #verify options arg_pass = _verifyOption(options) if not arg_pass: logging.warning(optparser.get_usage()) logging.critical("Non valid arguments: exit") sys.exit(1) utils_logging.change_log_stdout_to_log_stderr() if options.print_commands: utils_logging.change_log_stdout_to_log_stderr() else: command_runner.set_command_to_run_localy() run_fine = run_BWA_Command(options.genome_file, options.fastq_file1, options.fastq_file2, options.output_dir, options.name, analysis_type=options.analysis, sort=options.sort, thread=options.thread, read_group=options.read_group, illumina=options.illumina) if run_fine: logging.info('Run completed') else: logging.error('Run Failed') sys.exit(1)
def main(): #initialize the logging utils_logging.init_logging() #Setup options optparser=_prepare_optparser() (options,args) = optparser.parse_args() #verify options arg_pass=_verifyOption(options) utils_logging.change_log_stdout_to_log_stderr() if not arg_pass: logging.warning(optparser.get_usage()) logging.critical("Non valid arguments: exit") sys.exit(1) if options.mandatory_list_samples: mandatory_list_samples = options.mandatory_list_samples.split(',') else: mandatory_list_samples = None if options.list_samples: list_samples = options.list_samples.split(',') else: list_samples = None run_fine=vcf_to_simple_genotype(options.vcf_file, mandatory_list_samples, list_samples, options.nb_of_required_high_qual_genotype, options.print_all_genotype) if run_fine: logging.info('Run completed') else: logging.error('Run Failed') sys.exit(1)
def main(): #initialise the logging utils_logging.init_logging() #Setup options optparser=_prepare_optparser() (options,args) = optparser.parse_args() #verify options arg_pass=_verifyOption(options) if not arg_pass: logging.warning(optparser.get_usage()) logging.critical("Non valid arguments: exit") sys.exit(1) utils_logging.change_log_stdout_to_log_stderr() if options.wiki: parse_process_radtag_for_wiki(options.log_process_radtags, options.pools) else: parse_process_radtag(options.log_process_radtags, options.pools, options.project_id)
def main(): #initialize the logging utils_logging.init_logging() #Setup options optparser=_prepare_optparser() (options,args) = optparser.parse_args() #verify options arg_pass=_verifyOption(options) if not arg_pass: logging.warning(optparser.get_usage()) logging.critical("Non valid arguments: exit") sys.exit(1) utils_logging.change_log_stdout_to_log_stderr() bam_files=[options.bam_files] for file in args: if os.path.exists(file): bam_files.append(file) RAD_median_coverage(bam_files,options.output_file)