def create_html(dataset, output_html_dir, org_html, project_name, config):
import paplot.subcode.tools as tools
import os
chart_txt = ""
js_txt = ""
for i in range(len(dataset["plots"])):
chart_txt += html_chart_template.format(chart_id = dataset["plots"][i])
js_txt += html_js_template.format(i = str(i), chart_id = dataset["plots"][i])
if dataset["plots"][i] == "chart_brush":
js_txt += html_js_brushed_template.format(i = str(i))
f_template = open(os.path.dirname(os.path.abspath(__file__)) + "/templates/" + org_html)
html_template = f_template.read()
f_template.close()
f_html = open(output_html_dir + "/" + org_html, "w")
f_html.write(
html_template.format(project = project_name,
version = tools.version_text(),
date = tools.now_string(),
charts = chart_txt,
js_add_div = js_txt,
style = "../style/%s" % os.path.basename(tools.config_getpath(config, "style", "path", "default.js")),
))
f_html.close()
def create_html(dataset, output_html_dir, org_html, project_name, config):
import os
div_txt = ""
call_txt = ""
detail_txt = ""
for i in range(len(dataset["id_list"])):
div_txt += li_template.format(id = str(i), title = dataset["id_list"][i])
call_txt += call_template.format(id = str(i), title = dataset["id_list"][i])
detail_txt += detail_template.format(id = str(i), title = dataset["id_list"][i])
f_template = open(os.path.dirname(os.path.abspath(__file__)) + "/templates/" + org_html)
html_template = f_template.read()
f_template.close()
f_html = open(output_html_dir + "/" + org_html, "w")
f_html.write(
html_template.format(project = project_name,
version = tools.version_text(),
date = tools.now_string(),
div_list = div_txt,
call_list = call_txt,
details = detail_txt,
style = "../style/%s" % os.path.basename(tools.config_getpath(config, "style", "path", "default.js")),
))
f_html.close()
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 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 create_index(output_dir, project_name, config):
link_qc = """<li><a href="{project}/graph_qc.html" target=_blank>QC graphs</a>......Quality Control of bam.</li>
"""
link_sv = """<li><a href="{project}/graph_ca.html" target=_blank>CA graphs</a>......Chromosomal Aberration.</li>
"""
link_mut = """<li><a href="{project}/graph_mut.html" target=_blank>Mutation matrix</a>......Gene-sample mutational profiles.</li>
"""
link_sv_nodata = """<li>CA graphs......No Data.</li>
"""
link_mut_nodata = """<li>Mutation matrix......No Data.</li>
"""
import paplot.subcode.tools as tools
import os
f_template = open(os.path.dirname(os.path.abspath(__file__)) + "/templates/index.html")
html_template = f_template.read()
f_template.close()
link_text = ""
if os.path.exists(output_dir + "/" + project_name + "/graph_qc.html") == True:
link_text += link_qc.format(project = project_name)
if os.path.exists(output_dir + "/" + project_name + "/graph_ca.html") == True:
link_text += link_sv.format(project = project_name)
elif os.path.exists(output_dir + "/" + project_name + "/data_ca.csv") == True:
link_text += link_sv_nodata
if os.path.exists(output_dir + "/" + project_name + "/graph_mut.html") == True:
link_text += link_mut.format(project = project_name)
elif os.path.exists(output_dir + "/" + project_name + "/data_mut.csv") == True:
link_text += link_mut_nodata
f_html = open(output_dir + "/index.html", "w")
f_html.write(
html_template.format(project = project_name,
version = tools.version_text(),
date = tools.now_string(),
remarks = tools.config_getstr(config, "style", "remarks"),
link = link_text
))
f_html.close()
def create_html(dataset, output_html_dir, org_html, project_name, config):
import os
import paplot.subcode.tools as tools
sub1_text = ""
sub2_text = ""
set_sub_add_text = ""
set_sub_select_text = ""
for i in range(len(dataset["subdata"])):
sub_text = subplot_template.format(i = i, title = dataset["subdata"][i]["title"])
if dataset["subdata"][i]["pos"] == 1:
sub1_text += sub_text
set_sub_add_text += js_set_sub_add.format(i = i, type = 1)
else:
sub2_text += sub_text
set_sub_add_text += js_set_sub_add.format(i = i, type = 2)
set_sub_select_text += js_set_sub_select.format(i = i)
f_template = open(os.path.dirname(os.path.abspath(__file__)) + "/templates/" + org_html)
html_template = f_template.read()
f_template.close()
f_html = open(output_html_dir + "/" + org_html, "w")
f_html.write(
html_template.format(project = project_name,
version = tools.version_text(),
date = tools.now_string(),
sub1 = sub1_text,
sub2 = sub2_text,
set_sub_add = set_sub_add_text,
set_sub_select = set_sub_select_text,
style = "../style/%s" % os.path.basename(tools.config_getpath(config, "style", "path", "default.js")),
))
f_html.close()