def conf_main(args):
# config
[config,
conf_file] = tools.load_config(tools.win_to_unix(args.config_file))
tools.print_conf(config, conf_file, "paplot")
def main(argv):
import paplot.subcode.tools as tools
import paplot.subcode.merge as merge
import paplot.mut as mut
import paplot.prep as prep
import argparse
parser = argparse.ArgumentParser(prog = prog)
parser.add_argument("--version", action = "version", version = tools.version_text())
parser.add_argument("input", help = "input files path", type = str)
parser.add_argument("output_dir", help = "output file path", type = str)
parser.add_argument("project_name", help = "project name", type = str)
parser.add_argument("--config_file", help = "config file", type = str, default = "")
parser.add_argument("--remarks", help = "optional text", type = str, default = "")
args = parser.parse_args(argv)
# config
if len(args.config_file) > 0:
[config, conf_file] = tools.load_config(tools.win_to_unix(args.config_file))
else:
[config, conf_file] = tools.load_config("")
if len(args.remarks) > 0:
tools.config_set(config, "style", "remarks", args.remarks)
input_list = tools.get_inputlist(args.input)
if len(input_list) == 0:
print ("input no file.")
return
[sec_in, sec_out] = tools.get_section("mutation")
id_list = tools.get_IDlist(input_list, tools.config_getstr(config, sec_in, "suffix"))
# dirs
output_html_dir = prep.create_dirs(tools.win_to_unix(args.output_dir), args.project_name, config)
positions = merge.merge_result(input_list, id_list, output_html_dir + "/data_mut.csv", "mutation", config, extract = True)
if positions == {}:
print ("merge.merge_result: input file is invalid.")
return
mut.output_html(output_html_dir + "/data_mut.csv", output_html_dir + "/data_mut.js", \
output_html_dir, "graph_mut.html", args.project_name, positions, config)
prep.create_index(args.output_dir, args.project_name, config)
def pmsignature_main(args):
import paplot.pmsignature as pmsignature
# config
[config,
conf_file] = tools.load_config(tools.win_to_unix(args.config_file))
input_list = tools.get_inputlist(tools.win_to_unix(args.input))
if len(input_list) == 0:
print("input no file.")
return
# dirs
output_html_dir = prep.create_dirs(tools.win_to_unix(args.output_dir),
args.project_name, config)
for input_file in input_list:
params_in = {
"dir": output_html_dir,
"data": input_file,
"project": args.project_name,
"title": args.title,
"ellipsis": args.ellipsis,
}
params_out = pmsignature.output_html(params_in, config)
if params_out is None:
continue
if params_out == {}:
prep.create_index(config,
tools.win_to_unix(args.output_dir),
"",
args.project_name,
args.title,
overview=args.overview,
sub_text="",
composite=True,
remarks=args.remarks)
continue
sig_num_sift = 0
if tools.config_getboolean(config, "result_format_pmsignature",
"background"):
sig_num_sift = 1
prep.create_index(config,
tools.win_to_unix(args.output_dir),
params_out["html"],
args.project_name,
args.title,
overview=args.overview,
sub_text="#sig %d" %
(params_out["sig_num"] + sig_num_sift),
composite=True,
remarks=args.remarks)
def index_main(args):
# config
[config,
conf_file] = tools.load_config(tools.win_to_unix(args.config_file))
# dirs
output_dir = os.path.abspath(args.output_dir)
if (os.path.exists(output_dir) == False):
os.makedirs(output_dir)
prep.recreate_index(config,
tools.win_to_unix(args.output_dir),
remarks=args.remarks)
def qc_main(args):
import paplot.qc as qc
# config
[config,
conf_file] = tools.load_config(tools.win_to_unix(args.config_file))
input_list = tools.get_inputlist(tools.win_to_unix(args.input))
if len(input_list) == 0:
print("input no file.")
return
[sec_in, sec_out] = tools.get_section("qc")
id_list = tools.get_idlist(input_list,
tools.config_getstr(config, sec_in, "suffix"))
# dirs
output_html_dir = prep.create_dirs(tools.win_to_unix(args.output_dir),
args.project_name, config)
output_data = "data_%s%s" % (args.ellipsis, os.path.splitext(
input_list[0])[1])
positions = merge.merge_result(input_list,
id_list,
output_html_dir + "/" + output_data,
"qc",
config,
extract=True)
if positions == {}:
print("merge.merge_result: input file is invalid.")
return
html_name = "graph_%s.html" % args.ellipsis
params_html = {
"dir": output_html_dir,
"data": output_data,
"js": "data_%s.js" % args.ellipsis,
"html": html_name,
"project": args.project_name,
"title": args.title,
}
qc.output_html(params_html, positions, config)
prep.create_index(config,
tools.win_to_unix(args.output_dir),
html_name,
args.project_name,
args.title,
overview=args.overview,
remarks=args.remarks)
def main(argv):
import paplot.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, "paplot")
def ca_main(args):
'''
ca main script
Parameters
----------
args: argparse.Namespace
: Args contains the arguments specified in the paplot command
Args parameters
----------
input : string : Input file path
output_dir : string : Output directory path
project_name: string : Project name path
config_file : string : Config file path
title : string : Report title name
ellipsis : string : File name identifier for report
overview : string : Report summary
remarks : string : Additional information about report
func : function: This function (ca_main)
Return
------
None
'''
# The default values of the variables are defined in the file: ../../paplot
# config_file: "" :
# title : "CA graphs" : This value is replaced by {title} in ./templates/graph_ca.html
# ellipsis : "ca" : This value is used as part of file names, such as graph_ca.html
# overview : "Chromosomal Aberration.": This value is used in _convert_index_item function in ./prep.py
# remarks : "" : This value is replaced by {remarks} in ./templates/index.html
import paplot.ca as ca
# config
[config,
conf_file] = tools.load_config(tools.win_to_unix(args.config_file))
# input_list: a list with input data files as elements
input_list = tools.get_inputlist(tools.win_to_unix(args.input))
if len(input_list) == 0:
print("input no file.")
return
[sec_in, sec_out] = tools.get_section("ca")
# id_list is used when the column candidates defined in the config file are not in the header of input files
# see ids veriable of with_header function in ./subcode/merge.py for details
id_list = tools.get_idlist(input_list,
tools.config_getstr(config, sec_in, "suffix"))
# output_html_dir: The absolute path of the project directory
# output_data : File name like data_ca.csv
# : This file is created by the merge.merge_result function and placed in the project directory
# : The contents of the file are formatted from the input file to match the configuration file
# : After that, read the contents and convert it to Json format in ca.output_html function
# positions : A nested dictionary: {'must' : {key1: title1, ...}, 'option': {key2: title2, ...}}
output_html_dir = prep.create_dirs(tools.win_to_unix(args.output_dir),
args.project_name, config)
output_data = "data_%s%s" % (args.ellipsis, os.path.splitext(
input_list[0])[1])
positions = merge.merge_result(input_list,
id_list,
output_html_dir + "/" + output_data,
"ca",
config,
extract=True)
if positions == {}:
print("merge.merge_result: input file is invalid.")
return
# Create JavaScript file and HTML file for CA
html_name = "graph_%s.html" % args.ellipsis
params_html = {
"dir": output_html_dir, # Project directory full path
"data": output_data, # Data file name like csv
"js": "data_%s.js" % args.ellipsis, # JavaScript file name
"html": html_name, # HTML file name
"project":
args.project_name, # Project name given by user on command line
"title": args.title, # 'CA graphs' as default
}
ca.output_html(params_html, positions, config)
# Create homepage
prep.create_index(config,
tools.win_to_unix(args.output_dir),
html_name,
args.project_name,
args.title,
overview=args.overview,
remarks=args.remarks)
