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 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 copy_dir_style(dst, config):
import paplot.subcode.tools as tools
import shutil
import os
import glob
pattern = os.path.dirname(os.path.abspath(__file__)) + "/style/*"
li_files = glob.glob(pattern)
for f in li_files:
shutil.copy(f, dst)
# for option file
option = tools.config_getpath(config, "style", "path")
if len(option) > 0:
shutil.copy(option, dst)
def copy_dir_style(dst, config):
import paplot.subcode.tools as tools
import shutil
import os
import glob
pattern = os.path.dirname(os.path.abspath(__file__)) + "/style/*"
li_files = glob.glob(pattern)
for f in li_files:
shutil.copy(f, dst)
# for option file
option = tools.config_getpath(config, "style", "path")
if len(option) > 0:
shutil.copy(option, dst)
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_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 copy_dir_style(dst, config):
"""Copy ./style directory to the destination directory"""
import paplot.subcode.tools as tools
import shutil
import os
import glob
pattern = os.path.dirname(
os.path.abspath(__file__)) + "/style/*" # ./style/*
li_files = glob.glob(pattern)
for f in li_files:
shutil.copy(f, dst)
# for option file
option = tools.config_getpath(config, "style",
"path") # Additional style file
if len(option) > 0:
shutil.copy(option, dst)
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 load_subdata(ids, sec, config):
import os
import paplot.subcode.tools as tools
import paplot.convert as convert
import paplot.color as color
input_file = tools.config_getpath(config, sec, "path", default = "")
if os.path.exists(input_file) == False:
print ("[ERROR] file is not exist. %s" % input_file)
return None
sept = tools.config_getstr(config, sec, "sept").replace("\\t", "\t").replace("\\n", "\n").replace("\\r", "\r")
mode = tools.config_getstr(config, sec, "mode")
comment = tools.config_getstr(config, sec, "comment")
title = tools.config_getstr(config, sec, "title")
label = []
item = []
colors_n_di = {}
colors_h_di = {}
for name_set in tools.config_getstr(config, sec, "name_set").split(","):
name_set_split = convert.text_to_list(name_set, ":")
for i in range(len(name_set_split)):
text = name_set_split[i]
if i == 0:
item.append(text)
if len(name_set_split) == 1:
label.append(text)
elif i == 1:
label.append(text)
elif i == 2:
colors_n_di[name_set_split[0]] = color.name_to_value(text)
elif i == 3:
colors_h_di[name_set_split[0]] = color.name_to_value(text)
# fill in undefined items
colors_n_di = color.create_color_dict(item, colors_n_di, color.osaka_subway_colors)
colors_h_di2 = {}
for key in colors_n_di:
if key in colors_h_di: continue
colors_h_di2[key] = color.saturation_down(colors_n_di[key])
# dict to value
colors_n = []
for key in item:
colors_n.append(colors_n_di[key])
if mode == "range":
item.remove(item[0])
header = []
if tools.config_getboolean(config, sec, "header") == True:
pos_value = -1
pos_id = -1
else:
pos_value = tools.config_getint(config, sec, "col_value")-1
pos_id = tools.config_getint(config, sec, "col_ID")-1
header = ["",""]
# copy id_list for find check
unlookup = []
for iid in ids:
unlookup.append(iid)
# read
data_text = ""
values = []
for line in open(input_file):
line = line.strip()
if len(line.replace(sept, "")) == 0:
continue
if comment != "" and line.find(comment) == 0:
continue
if len(header) == 0:
header = convert.text_to_list(line,sept)
try:
colname = tools.config_getstr(config, sec, "col_value")
pos_value = header.index(colname)
colname = tools.config_getstr(config, sec, "col_ID")
pos_id = header.index(colname)
except Exception as e:
print(e.message)
return None
continue
cols = convert.text_to_list(line,sept)
if (cols[pos_id] in ids) == False: continue
else: unlookup.remove(cols[pos_id])
id_pos = ids.index(cols[pos_id])
if mode == "fix":
if cols[pos_value] in item:
data_text += subdata_data_template.format(id = id_pos, item = item.index(cols[pos_value]))
else:
print("[" + sec + "] name_set: data is undefined." + cols[pos_value] + "\n")
continue
elif mode == "range" or mode == "gradient":
try:
values.append(float(cols[pos_value]))
except Exception as e:
print(colname + ": data type is invalid.\n" + e.message)
continue
data_text += subdata_data_template.format(id = id_pos, item = cols[pos_value])
if len(unlookup) > 0:
print("[WARNING] can't find IDs subplot data.")
print(unlookup)
if mode == "gradient" and len(values) > 0:
item[0] = min(values)
item[1] = max(values)
return [data_text, item, colors_n, label, title]
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 load_genome_size(config):
"""
Read and parse a genome-size file and return a nested list:
[ [ A chromosome number in lowercase letters,
The size of the 1st element,
The color of the 1st element,
The original name of the 1st element(that is not necessarily lowercase) or a user-defined name,
],
...
]
"""
import os
import paplot.subcode.tools as tools
default_path = os.path.dirname(os.path.abspath(__file__)) + "/templates/genome_size_hg19.csv" # ./templates/genome_size_hg19.csv
path = tools.config_getpath(config, "genome", "path", default_path)
# Create a list with Name:Label:Color for each element
# Name is like chromosome number such as 1, 2, ..., X, Y, ...
# :Label and :Color is optional
settings = tools.config_getstr(config, "ca", "use_chrs").replace(" ", "").split(",")
use_chrs = []
labels = []
colors = []
for i in range(len(settings)):
# items[0]: Name corresponding to chromosome number
# items[1]: Label
# items[2]: Color
items = settings[i].split(":")
use_chrs.append(items[0].lower()) # Conversion of chromosome number to lowercase
labels.append("")
colors.append("#BBBBBB") # gray
for j in range(len(items)):
if j == 0:
if items[j][0:3] == "chr":
use_chrs[i] = items[j][3:] # Remove the leading "chr"
elif j == 1:
labels[i] = items[j]
elif j == 2:
colors[i] = items[j]
if len(use_chrs) < 1:
return []
# Read genome size
f = open(path)
read = f.read()
f.close()
formatt = read.replace("\r", "\n").replace(" ", "")
genome_size = []
_max = 0
for row in formatt.split("\n"):
# Delimiter setting
sept = ","
if row.find(",") < 0:
sept = "\t"
# Split the line and the second element must be numeric
# item[0]: chromosome number
# item[1]: size of item[0]
items = row.split(sept)
if len(items) < 2:
continue
if items[1].isdigit() is False:
continue
# The first element must be included in the list of chromosome numbers extracted from the configuration file
label = items[0].lower() # Convert label to lowercase
if label[0:3] == "chr":
label = label[3:len(label)] # Remove the leading "chr"
if (label in use_chrs) is False:
continue
# Create a list that is an element of genome_size
# The list has the following elements
# 1st: A chromosome number in lowercase letters
# 2st: The size of the 1st element
# 3st: The color of the 1st element
# 4st: The original name of the 1st element(that is not necessarily lowercase) or a user-defined name
# genome_size is in the order read from the genome-size file instead of the configuration file
pos = use_chrs.index(label)
if labels[pos] == "":
labels[pos] = items[0]
genome_size.append([label, int(items[1]), colors[pos], labels[pos]])
# Maximum size of the chromosome
if _max < int(items[1]):
_max = int(items[1])
# The minimum size of the chromosomes is set to 1/10 of the maximum size
for i in range(len(genome_size)):
if genome_size[i][1] < int(_max / 10):
genome_size[i][1] = int(_max / 10)
return genome_size
def load_genome_size(config):
path = tools.config_getpath(config, "genome", "path", "../../config/hg19.csv")
settings = tools.config_getstr(config, "sv", "use_chrs").replace(" ", "").split(",")
use_chrs = [];
colors = [];
labels = [];
for i in range(len(settings)):
items = settings[i].split(":")
use_chrs.append(items[0].lower())
labels.append("")
colors.append("#BBBBBB")
for j in range(len(items)):
if j == 0:
if items[j][0:3] == "chr":
use_chrs[i] = items[j][3:]
elif j == 1:
labels[i] = items[j]
elif j == 2:
colors[i] = items[j]
if len(use_chrs) < 1:
return []
f = open(path)
read = f.read()
f.close()
formatt = read.replace("\r", "\n").replace(" ", "")
genome_size = []
_max = 0
for row in formatt.split("\n"):
sept = ","
if row.find(",") < 0:
sept = "\t"
items = row.split(sept)
if len(items) < 2:
continue
if items[1].isdigit() == False:
continue
label = items[0].lower()
if label[0:3] == "chr":
label = label[3:len(label)]
if (label in use_chrs) == False:
continue
pos = use_chrs.index(label)
if _max < int(items[1]):
_max = int(items[1])
if labels[pos] == "":
labels[pos] = items[0]
genome_size.append([label, int(items[1]), colors[pos], labels[pos]])
for i in range(len(genome_size)):
if genome_size[i][1] < int(_max/10):
genome_size[i][1] = int(_max/10)
return genome_size
def load_genome_size(config):
path = tools.config_getpath(config, "genome", "path",
"../../config/hg19.csv")
settings = tools.config_getstr(config, "ca",
"use_chrs").replace(" ", "").split(",")
use_chrs = []
colors = []
labels = []
for i in range(len(settings)):
items = settings[i].split(":")
use_chrs.append(items[0].lower())
labels.append("")
colors.append("#BBBBBB")
for j in range(len(items)):
if j == 0:
if items[j][0:3] == "chr":
use_chrs[i] = items[j][3:]
elif j == 1:
labels[i] = items[j]
elif j == 2:
colors[i] = items[j]
if len(use_chrs) < 1:
return []
f = open(path)
read = f.read()
f.close()
formatt = read.replace("\r", "\n").replace(" ", "")
genome_size = []
_max = 0
for row in formatt.split("\n"):
sept = ","
if row.find(",") < 0:
sept = "\t"
items = row.split(sept)
if len(items) < 2:
continue
if items[1].isdigit() == False:
continue
label = items[0].lower()
if label[0:3] == "chr":
label = label[3:len(label)]
if (label in use_chrs) == False:
continue
pos = use_chrs.index(label)
if _max < int(items[1]):
_max = int(items[1])
if labels[pos] == "":
labels[pos] = items[0]
genome_size.append([label, int(items[1]), colors[pos], labels[pos]])
for i in range(len(genome_size)):
if genome_size[i][1] < int(_max / 10):
genome_size[i][1] = int(_max / 10)
return genome_size
def load_subdata(ids, sec, config):
import os
import paplot.subcode.tools as tools
import paplot.convert as convert
import paplot.color as color
input_file = tools.config_getpath(config, sec, "path", default = "../../example/sample_summary.csv")
if os.path.exists(input_file) == False:
print ("[ERROR] file is not exist. %s" % input_file)
return None
sept = tools.config_getstr(config, sec, "sept")
mode = tools.config_getstr(config, sec, "mode")
comment = tools.config_getstr(config, sec, "comment")
title = tools.config_getstr(config, sec, "title")
label = []
item = []
colors_n_di = {}
colors_h_di = {}
for name_set in tools.config_getstr(config, sec, "name_set").split(","):
name_set_split = convert.text_to_list(name_set, ":")
for i in range(len(name_set_split)):
text = name_set_split[i]
if i == 0:
item.append(text)
if len(name_set_split) == 1:
label.append(text)
elif i == 1:
label.append(text)
elif i == 2:
colors_n_di[name_set_split[0]] = color.name_to_value(text)
elif i == 3:
colors_h_di[name_set_split[0]] = color.name_to_value(text)
# fill in undefined items
colors_n_di = color.create_color_dict(item, colors_n_di, color.osaka_subway_colors)
colors_h_di2 = {}
for key in colors_n_di:
if colors_h_di.has_key(key): continue
colors_h_di2[key] = color.Saturation_down(colors_n_di[key])
# dict to value
colors_n = []
for key in item:
colors_n.append(colors_n_di[key])
if mode == "range":
item.remove(item[0])
header = []
if tools.config_getboolean(config, sec, "header") == True:
pos_value = -1
pos_ID = -1
else:
pos_value = tools.config_getint(config, sec, "col_value")
pos_ID = tools.config_getint(config, sec, "col_ID")
header = ["",""]
# copy Ids for find check
unlookup = []
for iid in ids:
unlookup.append(iid)
# read
data_text = ""
values = []
for line in open(input_file):
line = line.strip()
if len(line.replace(sept, "")) == 0:
continue
if comment != "" and line.find(comment) == 0:
continue
if len(header) == 0:
header = convert.text_to_list(line,sept)
try:
colname = tools.config_getstr(config, sec, "col_value")
pos_value = header.index(colname)
colname = tools.config_getstr(config, sec, "col_ID")
pos_ID = header.index(colname)
except Exception as e:
print(e.message)
return None
continue
cols = convert.text_to_list(line,sept)
if (cols[pos_ID] in ids) == False: continue
else: unlookup.remove(cols[pos_ID])
id_pos = ids.index(cols[pos_ID])
if mode == "fix":
if cols[pos_value] in item:
data_text += subdata_data_template.format(id = id_pos, item = item.index(cols[pos_value]))
else:
print("[" + sec + "] name_set: data is undefined." + cols[pos_value] + "\n")
continue
elif mode == "range":
try:
values.append(float(cols[pos_value]))
except Exception as e:
print(colname + ": data type is invalid.\n" + e.message)
continue
data_text += subdata_data_template.format(id = id_pos, item = cols[pos_value])
elif mode == "gradient":
try:
values.append(float(cols[pos_value]))
except Exception as e:
print(colname + ": data type is invalid.\n" + e.message)
continue
data_text += subdata_data_template.format(id = id_pos, item = cols[pos_value])
if len(unlookup) > 0:
print("[WARNING] can't find IDs subplot data.")
print(unlookup)
if mode == "gradient" and len(values) > 0:
item[0] = min(values)
item[1] = max(values)
return [data_text, item, colors_n, label, title]
