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 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 recreate_index(config, output_dir, remarks = ""):
import paplot.subcode.tools as tools
import os
json_data = _reload_metadata(output_dir)
link_text = _convert_index_item(json_data)
f_template = open(os.path.dirname(os.path.abspath(__file__)) + "/templates/index.html")
html_template = f_template.read()
f_template.close()
if remarks == "":
remarks = tools.config_getstr(config, "style", "remarks")
f_html = open(output_dir + "/index.html", "w")
f_html.write(
html_template.format(
version = version_text(),
date = tools.now_string(),
remarks = remarks,
link = link_text
)
)
f_html.close()
def create_html(dataset, output_di, config):
import paplot.subcode.tools as tools
import paplot.prep as prep
import os
chart_txt = ""
js_txt = ""
for i in range(len(dataset["plots"])):
js_txt += html_js_template.format(i=str(i), chart_id=dataset["plots"][i])
if dataset["plots"][i] == "chart_brush":
chart_txt += '<p class="muted pull-left" style="margin-right: 15px;">Select a range to zoom in</p>\n'
js_txt += html_js_brushed_template.format(i=str(i))
chart_txt += html_chart_template.format(chart_id=dataset["plots"][i])
f_template = open(os.path.dirname(os.path.abspath(__file__)) + "/templates/graph_qc.html")
html_template = f_template.read()
f_template.close()
f_html = open(output_di["dir"] + "/" + output_di["html"], "w")
f_html.write(
html_template.format(project=output_di["project"],
title=output_di["title"],
data_js=output_di["js"],
version=prep.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_index(config, output_dir, output_html, project_name, name, overview = "", sub_text = "", composite = False, remarks = ""):
import paplot.subcode.tools as tools
import os
html_exists = os.path.exists(output_dir + "/" + project_name + "/" + output_html)
if output_html == "":
html_exists = False
json_data = _load_metadata(output_dir, output_html, project_name, name, overview, sub_text, composite, html_exists)
link_text = _convert_index_item(json_data)
f_template = open(os.path.dirname(os.path.abspath(__file__)) + "/templates/index.html")
html_template = f_template.read()
f_template.close()
if remarks == "":
remarks = tools.config_getstr(config, "style", "remarks")
f_html = open(output_dir + "/index.html", "w")
f_html.write(
html_template.format(
version = version_text(),
date = tools.now_string(),
remarks = remarks,
link = link_text
)
)
f_html.close()
def create_html(dataset, params, config):
import os
import paplot.subcode.tools as tools
import paplot.prep as prep
html_div_template = "<div style='float: left;' id='div_pm{id}'></div>\n"
html_add_template = "msig_draw.add_div('div_pm{id}');\n"
div_text = ""
add_text = ""
for i in range(dataset["sig_num"]):
div_text += html_div_template.format(id=i)
add_text += html_add_template.format(id=i)
integral_text = ""
if dataset["intergral"] is True:
integral_text = html_integral_template
f_template = open(
os.path.dirname(os.path.abspath(__file__)) +
"/templates/graph_pmsignature.html")
html_template = f_template.read()
f_template.close()
sig_num_sift = 0
if tools.config_getboolean(config, "result_format_pmsignature",
"background"):
sig_num_sift = 1
f_html = open(params["dir"] + "/" + dataset["html"], "w")
f_html.write(
html_template.format(
project=params["project"],
title="%s(#sig %d)" %
(params["title"], dataset["sig_num"] + sig_num_sift),
data_js=dataset["js"],
version=prep.version_text(),
date=tools.now_string(),
divs=div_text,
add_divs=add_text,
integral=integral_text,
style="../style/%s" % os.path.basename(
tools.config_getpath(config, "style", "path", "default.js")),
))
f_html.close()
def create_html(dataset, output_di, config):
import os
import paplot.subcode.tools as tools
import paplot.prep as prep
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/graph_mutation.html")
html_template = f_template.read()
f_template.close()
f_html = open(output_di["dir"] + "/" + output_di["html"], "w")
f_html.write(
html_template.format(
project=output_di["project"],
title=output_di["title"],
data_js=output_di["js"],
version=prep.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()
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_di, config):
import os
import paplot.prep as prep
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])
detail_txt += detail_template.format(id=str(i),
title=dataset["id_list"][i])
call_txt += call_template.format(id=str(i),
title=dataset["id_list"][i])
# if i >= 50:
# if i == 50:
# call_txt += call_later_header
# call_txt += call_later_template.format(id = str(i), title = dataset["id_list"][i])
# else:
# call_txt += call_template.format(id = str(i), title = dataset["id_list"][i])
f_template = open(
os.path.dirname(os.path.abspath(__file__)) +
"/templates/graph_ca.html")
html_template = f_template.read()
f_template.close()
f_html = open(output_di["dir"] + "/" + output_di["html"], "w")
f_html.write(
html_template.format(
project=output_di["project"],
title=output_di["title"],
data_js=output_di["js"],
version=prep.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 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()
def create_html(dataset, output_di, config):
"""
Create HTML file for CA
Parameters
----------
dataset: dict: {"id_list" : [id column values],
"group_list": [group names],
"color" : [group colors]}
output_di: dict: {"dir" : project directory full path,
"data" : filenames for formatted data
"js" : JavaScript file name
"html" : HTML file name
"project": Project name given by user on command line
"title" : Report title. The default is "CA graphs"}
config: configparser.RawConfigParser
Return
------
None
"""
import os
import paplot.prep as prep
import paplot.subcode.tools as tools
# Create strings of thumbnails to embed in HTML
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]) # Rough thumbnail
detail_txt += detail_template.format(id=str(i), title=dataset["id_list"][i]) # Detailed thumbnail
call_txt += call_template.format(id=str(i), title=dataset["id_list"][i]) # Drawing rough thumbnail
# if i >= 50:
# if i == 50:
# call_txt += call_later_header
# call_txt += call_later_template.format(id = str(i), title = dataset["id_list"][i])
# else:
# call_txt += call_template.format(id = str(i), title = dataset["id_list"][i])
# Overlay
overlay_txt = overlay_template.format(id=str(len(dataset["id_list"])))
# Get HTML template
f_template = open(os.path.dirname(os.path.abspath(__file__)) + "/templates/graph_ca.html") # ./templates/graph_ca.html
html_template = f_template.read()
f_template.close()
# Create HTML file
f_html = open(output_di["dir"] + "/" + output_di["html"], "w") # Create a file under the project directory
f_html.write(
html_template.format(
project=output_di["project"], # Project name
title=output_di["title"], # Report title
data_js=output_di["js"], # JavaScript file
version=prep.version_text(), # Paplot version
date=tools.now_string(), # Cuurent time
div_list=div_txt, # Rough thumbnail
details=detail_txt, # Detailed thumbnail
overlay=overlay_txt, # Overlay thumbnail
call_list=call_txt, # Drawing rough thumbnail
style="../style/%s" % os.path.basename(tools.config_getpath(config, "style", "path", "default.js")), # ./style/default.js
))
f_html.close()
def create_index(config,
output_dir,
output_html,
project_name,
name,
overview="",
sub_text="",
composite=False,
remarks=""):
"""
Create homepage
Parameters
----------
config : configparser.RawConfigParser
output_dir : string: Output directory path
output_html : string: HTML file name
project_name: string: Project name given by user on command line
name : string: Report title
overview : string: Report summary
sub_text : string: Additional string to display if composite=True and a report does not exist
composite : bool : Whether or not to have multiple reports
remarks : string: Additional information about report
Return
----------
None
"""
import paplot.subcode.tools as tools
import os
# Confirm existence of homepage
html_exists = os.path.exists(output_dir + "/" + project_name + "/" +
output_html)
if output_html == "":
html_exists = False
# Create json data
json_data = _load_metadata(output_dir, output_html, project_name, name,
overview, sub_text, composite, html_exists)
# Create html for link
link_text = _convert_index_item(json_data)
# Load the template html for the homepage
f_template = open(
os.path.dirname(os.path.abspath(__file__)) +
"/templates/index.html") # ./templates/index.html
html_template = f_template.read()
f_template.close()
# Extract remarks from a configuration
if remarks == "":
remarks = tools.config_getstr(config, "style", "remarks")
# Create html file for a homepage
f_html = open(output_dir + "/index.html", "w")
f_html.write(
html_template.format(
version=version_text(), # Version
date=tools.now_string(), # Current time
remarks=remarks, # Some string
link=link_text) # HTML for link
)
f_html.close()
