def convert_tojs(params, config):
import os
import json
import paplot.subcode.tools as tools
import paplot.convert as convert
import paplot.color as color
# data read
try:
json_data = json.load(open(params["data"]))
except Exception as e:
print("failure open data %s, %s" % (params["data"], e.message))
return None
key_id_list = tools.config_getstr(config, "result_format_pmsignature",
"key_id")
key_ref = tools.config_getstr(config, "result_format_pmsignature",
"key_ref")
key_alt = tools.config_getstr(config, "result_format_pmsignature",
"key_alt")
key_strand = tools.config_getstr(config, "result_format_pmsignature",
"key_strand")
key_mutations = tools.config_getstr(config, "result_format_pmsignature",
"key_mutation")
key_mutation_count = tools.config_getstr(config,
"result_format_pmsignature",
"key_mutation_count")
sig_num = len(json_data[key_ref])
if sig_num == 0:
print("no data %s" % params["data"])
return {}
# signature names
signature_list = []
for s in range(sig_num):
signature_list.append("Signature %d" % (s + 1))
# each signature colors
sig_color_list = color.create_color_array(sig_num, color.r_set2)
# use background?
if tools.config_getboolean(config, "result_format_pmsignature",
"background"):
signature_list.append("Background ")
sig_color_list.append(color.r_set2_gray)
# Id list
id_txt = ""
if key_id_list in json_data:
id_txt = convert.list_to_text(json_data[key_id_list])
# mutations
mutations_txt = ""
if key_mutations in json_data:
for m in json_data[key_mutations]:
mutations_txt += "[%d,%d,%f]," % (m[0], m[1], m[2])
# signature
dataset_ref = ""
for sig in json_data[key_ref]:
tmp = ""
for sub in sig:
tmp += "[" + ",".join(map(str, sub)) + "],"
dataset_ref += ("[" + tmp + "],")
dataset_alt = ""
for sig in json_data[key_alt]:
tmp = ""
for sub in sig:
tmp += "[" + ",".join(map(str, sub)) + "],"
dataset_alt += ("[" + tmp + "],")
dataset_strand = ""
for sig in json_data[key_strand]:
dataset_strand += "[" + ",".join(map(str, sig)) + "],"
# tooltips
# for ref
keys_di = {
"a": "",
"c": "",
"g": "",
"t": "",
"ca": "",
"cg": "",
"ct": "",
"ta": "",
"tc": "",
"tg": "",
"plus": "",
"minus": "",
"id": "",
"sig": ""
}
tooltip_refs_txt = ""
for r in range(len(json_data[key_ref][0])):
tooltip_refs_txt += js_tooltip_ref_template.format(
index=r,
tooltip_format=convert.pyformat_to_jstooltip_text(
keys_di, config, "pmsignature", "", "tooltip_format_ref"))
mutation_count_txt = ""
if (key_mutation_count != "") and (key_mutation_count in json_data.keys()):
for v in json_data[key_mutation_count]:
mutation_count_txt += "%d," % v
# output
sig_num_sift = 0
if tools.config_getboolean(config, "result_format_pmsignature",
"background"):
sig_num_sift = 1
ellipsis = "%s%d" % (params["ellipsis"], (sig_num + sig_num_sift))
js_file = "data_%s.js" % ellipsis
html_file = "graph_%s.html" % ellipsis
f = open(params["dir"] + "/" + js_file, "w")
f.write(js_header + js_dataset.format(
Ids=id_txt,
color_A=tools.config_getstr(config, "pmsignature", "color_A",
"#06B838"),
color_C=tools.config_getstr(config, "pmsignature", "color_C",
"#609CFF"),
color_G=tools.config_getstr(config, "pmsignature", "color_G",
"#B69D02"),
color_T=tools.config_getstr(config, "pmsignature", "color_T",
"#F6766D"),
color_plus=tools.config_getstr(config, "pmsignature", "color_plus",
"#00BEC3"),
color_minus=tools.config_getstr(config, "pmsignature", "color_minus",
"#F263E2"),
signatures=convert.list_to_text(signature_list),
colors=convert.list_to_text(sig_color_list),
mutations=mutations_txt,
dataset_ref=dataset_ref,
dataset_alt=dataset_alt,
dataset_strand=dataset_strand,
tooltip_ref=tooltip_refs_txt,
tooltip_alt=convert.pyformat_to_jstooltip_text(
keys_di, config, "pmsignature", "", "tooltip_format_alt"),
tooltip_strand=convert.pyformat_to_jstooltip_text(
keys_di, config, "pmsignature", "", "tooltip_format_strand"),
mutation_title=convert.pyformat_to_jstooltip_text(
keys_di, config, "pmsignature", "",
"tooltip_format_mutation_title"),
mutation_partial=convert.pyformat_to_jstooltip_text(
keys_di, config, "pmsignature", "",
"tooltip_format_mutation_partial"),
mutation_count=mutation_count_txt,
))
f_template = open(
os.path.dirname(os.path.abspath(__file__)) +
"/templates/data_pmsignature.js")
js_function = f_template.read()
f_template.close()
f.write(js_function)
f.write(js_footer)
f.close()
integral = True
if key_id_list == "" or key_mutations == "" or key_mutation_count == "":
integral = False
return {
"sig_num": sig_num,
"js": js_file,
"html": html_file,
"intergral": integral,
}
def convert_tojs(params, config):
import json
import math
import itertools
import paplot.subcode.tools as tools
import paplot.convert as convert
import paplot.color as color
# data read
try:
jsonData = json.load(open(params["data"]))
except Exception as e:
print ("failure open data %s, %s" % (params["data"], e.message))
return None
key_Ids = tools.config_getstr(config, "result_format_signature", "key_id")
key_signature = tools.config_getstr(config, "result_format_signature", "key_signature")
key_mutations = tools.config_getstr(config, "result_format_signature", "key_mutation")
key_mutation_count = tools.config_getstr(config, "result_format_signature", "key_mutation_count")
sig_num = len(jsonData[key_signature])
if sig_num == 0:
print ("no data %s" % params["data"])
return {}
# signature names
signature_list = []
for s in range(sig_num):
signature_list.append("Signature %d" % (s+1))
# each signature colors
sig_color_list = color.create_color_array(sig_num, color.r_set2)
# use background?
if tools.config_getboolean(config, "result_format_signature", "background"):
signature_list.append("Background ")
sig_color_list.append(color.r_set2_gray)
# axis-y max
sig_y_max = tools.config_getint(config, "signature", "signature_y_max")
if (sig_y_max < 0):
for sig in jsonData[key_signature]:
for sub in sig:
m = max(sub)
if sig_y_max < m:
sig_y_max = m
# route list
sub_num = len(jsonData[key_signature][0][0])
log = math.log(sub_num, 4)
if log % 1 > 0:
print ("substitution's list length is invalid (%d, not number 4^N)" % sub_num)
return None
route_id = []
route_list = []
for p in itertools.product(("A","C","G","T"), repeat = int(log)):
route_id.append("".join(p))
route_list.append(p)
# substruction
sub_di = [
{"name":"C > A", "ref":"C", "color":tools.config_getstr(config, "signature", "alt_color_CtoA")},
{"name":"C > G", "ref":"C", "color":tools.config_getstr(config, "signature", "alt_color_CtoG")},
{"name":"C > T", "ref":"C", "color":tools.config_getstr(config, "signature", "alt_color_CtoT")},
{"name":"T > A", "ref":"T", "color":tools.config_getstr(config, "signature", "alt_color_TtoA")},
{"name":"T > C", "ref":"T", "color":tools.config_getstr(config, "signature", "alt_color_TtoC")},
{"name":"T > G", "ref":"T", "color":tools.config_getstr(config, "signature", "alt_color_TtoG")},
]
substruction = ""
for sub in sub_di:
route = []
for r in route_list:
route.append("p".join(r[0:int(log/2)]) + "p" + sub["ref"] + "p" + "p".join(r[int(log/2):]))
substruction += js_substruction_template.format(name = sub["name"], color = sub["color"], route = convert.list_to_text(route))
# Id list
id_txt = ""
if key_Ids in jsonData:
id_txt = convert.list_to_text(jsonData[key_Ids])
# mutations
mutations_txt = ""
if key_mutations in jsonData:
for m in jsonData[key_mutations]:
mutations_txt += "[%d,%d,%f]," % (m[0],m[1],m[2])
# signature
dataset_sig = ""
for sig in jsonData[key_signature]:
tmp = ""
for sub in sig:
tmp += "[" + ",".join(map(str, sub)) + "],"
dataset_sig += ("[" + tmp + "],")
mutation_count_txt = ""
if (key_mutation_count != "") and (key_mutation_count in jsonData.keys()):
for v in jsonData[key_mutation_count]:
mutation_count_txt += "%d," % v
# output
sig_num_sift = 0
if tools.config_getboolean(config, "result_format_signature", "background"):
sig_num_sift = 1
ellipsis = "%s%d" % (params["ellipsis"], (sig_num + sig_num_sift))
js_file = "data_%s.js" % ellipsis
html_file = "graph_%s.html" % ellipsis
keys_di = {"sig":"", "route":"", "id":""}
f = open(params["dir"] + "/" + js_file, "w")
f.write(js_header \
+ js_dataset.format(Ids = id_txt, \
signatures = convert.list_to_text(signature_list), \
colors = convert.list_to_text(sig_color_list), \
dataset_sig_max = sig_y_max, \
mutations = mutations_txt, \
dataset_sig = dataset_sig, \
route_id = convert.list_to_text(route_id), \
substruction = substruction, \
signature_title = convert.pyformat_to_jstooltip_text(keys_di, config, "signature", "", "tooltip_format_signature_title"), \
signature_partial = convert.pyformat_to_jstooltip_text(keys_di, config, "signature", "", "tooltip_format_signature_partial"), \
mutation_title = convert.pyformat_to_jstooltip_text(keys_di, config, "signature", "", "tooltip_format_mutation_title"), \
mutation_partial = convert.pyformat_to_jstooltip_text(keys_di, config, "signature", "", "tooltip_format_mutation_partial"), \
mutation_count = mutation_count_txt, \
)
+ js_function)
f.close()
integral = True
if key_Ids == "" or key_mutations == "" or key_mutation_count == "":
integral = False
return {"sig_num": sig_num,
"js": js_file,
"html": html_file,
"intergral": integral,
}