コード例 #1
0
ファイル: RAD_vcf_to_tsv.py プロジェクト: pamoran/RADmapper
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)
コード例 #2
0
ファイル: run_BWA_commands.py プロジェクト: tcezard/RADmapper
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)
コード例 #3
0
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)
コード例 #4
0
ファイル: RAD_vcf_to_tsv.py プロジェクト: tcezard/RADmapper
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)
コード例 #5
0
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)
コード例 #6
0
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)