def set_sample_2type(li, mode, config):
# tumor, control-panel
import genomon_post_analysis.subcode.tools as tools
tmr_list = []
tmr_none = []
[section_in, section_out] = tools.get_section(mode)
unpanel = tools.config_getboolean(config, section_out, "include_unpanel")
for item in li:
if item[1]== None: # control-panel
if unpanel == True: tmr_none.append(item[0])
else:
tmr_list.append(item[0])
sample_dict = {"all":[], "case1":[], "case2":[], "case3":[], "case4":[]}
if tools.config_getboolean(config, section_out, "all_in_one") == True:
al = []
al.extend(tmr_list)
al.extend(tmr_none)
sample_dict["all"] = al
if tools.config_getboolean(config, section_out, "separate") == True:
sample_dict["case1"] = tmr_list
sample_dict["case2"] = tmr_none
return sample_dict
def arg_to_file(mode, genomon_root, args, config):
def text_to_list(inputs, flg):
if flg == False:
return []
if len(inputs) == 0:
return []
f = inputs.lstrip("'").lstrip('"').rstrip("'").rstrip('"').split(";")
li = []
for item in f[0].split(","):
li.append(item.lstrip(" ").rstrip(" "))
return li
[section_in, section_out] = tools.get_section(mode)
sample_dict = {"all":[], "case1":[], "case2":[], "case3":[], "case4":[]}
if tools.config_getboolean(config, section_out, "all_in_one") == True:
al = []
al.extend(text_to_list(args.input_file_case1, True))
al.extend(text_to_list(args.input_file_case2, tools.config_getboolean(config, section_out, "include_unpanel")))
al.extend(text_to_list(args.input_file_case3, tools.config_getboolean(config, section_out, "include_unpair")))
al.extend(text_to_list(args.input_file_case4,
tools.config_getboolean(config, section_out, "include_unpair") and tools.config_getboolean(config, section_out, "include_unpanel")))
sample_dict["all"] = al
if tools.config_getboolean(config, section_out, "separate") == True:
sample_dict["case1"] = text_to_list(args.input_file_case1, True)
sample_dict["case2"] = text_to_list(args.input_file_case2, tools.config_getboolean(config, section_out, "include_unpanel"))
sample_dict["case3"] = text_to_list(args.input_file_case3, tools.config_getboolean(config, section_out, "include_unpair"))
sample_dict["case4"] = text_to_list(args.input_file_case4,
tools.config_getboolean(config, section_out, "include_unpair") and tools.config_getboolean(config, section_out, "include_unpanel"))
return sample_dict
def call_merge_result(mode, ids_dict, output_dir, genomon_root, config):
print "=== [%s] merge result file. ===" % mode
#import os
import genomon_post_analysis.subcode.merge as subcode_merge
import merge
[section_in, section_out] = tools.get_section(mode)
suffix_u = tools.config_getstr(config, section_in, "suffix")
suffix_f = tools.config_getstr(config, section_in, "suffix_filt")
merge_unfilt = tools.config_getboolean(config, section_out, "include_unfilt")
for key in ids_dict:
if len(ids_dict[key]) == 0:
continue
# unfilterd
output_name = tools.config_getstr(config, section_out, "output_" + key)
#if output_name != "" and os.path.exists(output_dir + "/" + output_name) == False:
if output_name != "":
if merge_unfilt == True:
files = []
for iid in ids_dict[key]:
files.append(capture.sample_to_result_file(iid, mode, genomon_root, suffix_u))
if mode == "mutation":
merge.merge_mutaion_for_paplot(files, ids_dict[key], output_dir + "/" + output_name, config)
elif mode == "starqc":
merge.merge_star_qc_for_paplot(files, ids_dict[key], output_dir + "/" + output_name, config)
else:
subcode_merge.merge_result(files, ids_dict[key], output_dir + "/" + output_name, mode, config)
# filterd
output_name = tools.config_getstr(config, section_out, "output_filt_" + key)
#if output_name != "" and os.path.exists(output_dir + "/" + output_name) == False:
if output_name != "":
files = []
for iid in ids_dict[key]:
files.append(capture.sample_to_result_file(iid, mode, genomon_root, suffix_f))
if mode == "mutation":
merge.merge_mutaion_for_paplot(files, ids_dict[key], output_dir + "/" + output_name, config)
elif mode == "starqc":
merge.merge_star_qc_for_paplot(files, ids_dict[key], output_dir + "/" + output_name, config)
else:
subcode_merge.merge_result(files, ids_dict[key], output_dir + "/" + output_name, mode, config)
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)
