def main(argv):
import genomon_post_analysis.subcode.tools as tools
import argparse
parser = argparse.ArgumentParser(prog = prog)
parser.add_argument("--version", action = "version", version = tools.version_text())
parser.add_argument("--config_file", help = "config file", type = str, default = "")
args = parser.parse_args(argv)
# config
[config, conf_file] = tools.load_config(args.config_file)
tools.print_conf(config, conf_file, "Genomon Post Analysis")
def main(mode, argv):
import os
import argparse
parser = argparse.ArgumentParser(prog = prog)
parser.add_argument("--version", action = "version", version = tools.version_text())
parser.add_argument('mode', choices=['dna', 'rna', 'mutation', 'sv', 'qc', 'fusion', 'starqc'], help = "analysis type")
parser.add_argument("output_dir", help = "output file path", type = str)
parser.add_argument("genomon_root", help = "Genomon root path", type = str)
parser.add_argument("sample_sheet", help = "sample file of Genomon", type = str)
parser.add_argument("--config_file", help = "config file", type = str, default = "")
# for genomon-call
parser.add_argument("--input_file_case1", help = "input file", type = str, default = "")
parser.add_argument("--input_file_case2", help = "input file", type = str, default = "")
parser.add_argument("--input_file_case3", help = "input file", type = str, default = "")
parser.add_argument("--input_file_case4", help = "input file", type = str, default = "")
parser.add_argument("--samtools", help = "samtool's path", type = str, default = "")
parser.add_argument("--bedtools", help = "bedtool's path", type = str, default = "")
args = parser.parse_args(argv)
# dirs
output_dir = os.path.abspath(args.output_dir)
if (os.path.exists(output_dir) == False):
os.mkdir(output_dir)
genomon_root = os.path.abspath(args.genomon_root)
# config
[config, conf_file] = tools.load_config(args.config_file)
sample_conf = capture.load_sample_conf(args.sample_sheet, False)
if sample_conf == None:
return
# call functions
if args.mode == "all":
if mode == "dna":
sample_dic = capture.sample_to_list(sample_conf, "sv", genomon_root, config)
if tools.config_getboolean(config, "igv", "enable") == True:
call_image_capture("sv", sample_dic, output_dir, genomon_root, sample_conf, config)
if tools.config_getboolean(config, "bam", "enable") == True:
call_bam_pickup("sv", sample_dic, output_dir, genomon_root, args.samtools, args.bedtools, sample_conf, config)
call_merge_result("sv", sample_dic, output_dir, genomon_root, config)
sample_dic = capture.sample_to_list(sample_conf, "mutation", genomon_root, config)
if tools.config_getboolean(config, "igv", "enable") == True:
call_image_capture("mutation", sample_dic, output_dir, genomon_root, sample_conf, config)
if tools.config_getboolean(config, "bam", "enable") == True:
call_bam_pickup("mutation", sample_dic, output_dir, genomon_root, args.samtools, args.bedtools, sample_conf, config)
call_merge_result("mutation", sample_dic, output_dir, genomon_root, config)
sample_dic = capture.sample_to_list(sample_conf, "qc", genomon_root, config)
call_merge_result("qc", sample_dic, output_dir, genomon_root, config)
elif mode == "rna":
sample_dic = capture.sample_to_list(sample_conf, "fusionfusion", genomon_root, config)
call_merge_result("fusion", sample_dic, output_dir, genomon_root, config)
sample_dic = capture.sample_to_list(sample_conf, "qc", genomon_root, config)
call_merge_result("starqc", sample_dic, output_dir, genomon_root, config)
else:
sample_dic = arg_to_file(args.mode, genomon_root, args, config)
num = 0
for key in sample_dic: num += len(sample_dic[key])
if num == 0:
sample_dic = capture.sample_to_list(sample_conf, args.mode, genomon_root, config)
if args.mode == "qc":
call_merge_result(args.mode, sample_dic, output_dir, genomon_root, config)
elif args.mode == "fusion":
call_merge_result(args.mode, sample_dic, output_dir, genomon_root, config)
elif args.mode == "starqc":
call_merge_result(args.mode, sample_dic, output_dir, genomon_root, config)
else:
if tools.config_getboolean(config, "igv", "enable") == True:
call_image_capture(args.mode, sample_dic, output_dir, genomon_root, sample_conf, config)
if tools.config_getboolean(config, "bam", "enable") == True:
call_bam_pickup(args.mode, sample_dic, output_dir, genomon_root, args.samtools, args.bedtools, sample_conf, config)
call_merge_result(args.mode, sample_dic, output_dir, genomon_root, config)
