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server.py
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from flask import Flask, request, render_template, Response, redirect, send_from_directory, session, \
copy_current_request_context
import vcf
# import base64
from io import BufferedReader, TextIOWrapper
# import bs4
import requests
# from pyensembl import EnsemblRelease
from ensembl import getGenesFromLocation, getGeneFromGeneId, getVariantFromLocation
from biothings_client import get_client
import json
import os
import csv
from multiprocessing import Process, Manager, Pool
from flask_session import Session
from json2html import *
from civicdb import CivicDb
from cosmicdb import CosmicDb
import traceback
import time
import mapping # mapping.remap()
import universalKeys as dictKeys # selected dict keys and their descriptions
import cadd
from collections import OrderedDict
import threading
app = Flask(__name__)
app.config['JSON_SORT_KEYS'] = False
app.secret_key = b'\xdd\xd6]j\xb0\xcc\xe3mNF{\x14\xaf\xa7\xb3\x18'
dbs = (102, 75, 54)
dbName = {
"54": "NCBI36",
"75": "GRCh37",
"102": "GRCh38"
}
# data = EnsemblRelease(102)
SESSION_TYPE = 'filesystem'
gene_client = get_client('gene')
variant_client = get_client('variant')
civic = CivicDb()
cosmic = CosmicDb()
manager = Manager()
app.config.from_object(__name__)
Session(app)
biothingsAssembly = "hg19"
tempSession = {}
ensembl_keys = {
"strand":"Strand",
"id": "Gene Id",
"start": "Gene Start",
"end": "Gene End",
"description": "Gene Description",
"biotype": "Gene Type",
"external_name": "Gene Name",
"mutation_description_aa": "Variant Type",
"consequence_type":"Variant Type"
}
@app.route("/")
def index():
if "stamp" in session:
print(time.time() - session["stamp"])
if "done" in session or ("stamp" in session and str(session["stamp"]) + "done" in tempSession):
if "done" in session:
del session["done"]
if "stamp" in session:
if session["stamp"] in tempSession:
del tempSession[session["stamp"]]
if str(session["stamp"]) + "done" in tempSession:
del tempSession[str(session["stamp"]) + "done"]
del session["stamp"]
if "stamp" in session and time.time() - session["stamp"] > 1000:
if session["stamp"] in tempSession:
del tempSession[session["stamp"]]
if str(session["stamp"]) + "done" in tempSession:
del tempSession[str(session["stamp"]) + "done"]
del session["stamp"]
return render_template("index.html")
def getGeneInfo(gene_id, table):
geneData = gene_client.getgene(gene_id)
if "summary" not in geneData:
table["Summary"] = ("")
else:
tm = time.time()
table["Summary"] = """
<p>
%s
</p>
<p class="%s" hidden>%s</p>
<a id="%s" href="javascript:toggleSummary('%s')">
Read More...
</a>
""" % (geneData["summary"][:37],tm,geneData["summary"],tm,tm)
if "entrezgene" not in geneData:
table["Entrezgene"] = ("")
else:
table["Entrezgene"] = ('<a target=\"_blank\" href="https://www.ncbi.nlm.nih.gov/gene/%s">%s</a>'
% (geneData["entrezgene"], geneData["entrezgene"]))
clinical_data = ""
if "clingen" in geneData and "clinical_validity" in geneData["clingen"]:
clinical_data = []
if type(geneData["clingen"]["clinical_validity"]) == dict:
clinical_data.append(geneData["clingen"]["clinical_validity"])
elif type(geneData["clingen"]["clinical_validity"]) == list:
for key in geneData["clingen"]["clinical_validity"]:
clinical_data.append(key)
table["Clingen"] = (clinical_data)
@app.route("/static/images/logom.png")
def logo():
print("logo asked for")
return send_from_directory(os.path.join(app.root_path, 'static', 'images'),
'logom.png', mimetype='image/png')
@app.route("/constructannotation", methods=["GET"])
def constructannotationGet():
return render_template("constructannotation.html",alert="")
@app.route("/constructannotation", methods=["POST"])
def constructannotation():
file = request.files["efile"]
print(file.name)
if not file.filename.endswith(".json"):
return render_template(
"/constructannotation.html",
alert = "File extension not matching"
)
#file = BufferedReader(file)
#file = TextIOWrapper(file)
try:
nnewtable = json.load(file)
except:
return render_template(
"/constructannotation.html",
alert="Corrupted file"
)
temp = {}
keys = ["General","Civic","Cosmic","Cadd"]
for key in nnewtable:
temp[key] = {}
for key2 in keys:
temp[key][key2] = []
for element in nnewtable[key][key2]:
temp[key][key2].append(element)
nnewtable = temp.copy()
print(nnewtable)
session["table"] = nnewtable.copy()
mainKeys = '''
<label for="Cosmic">
<input type="checkbox" id="Cosmic" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
Cosmic
</label>
<label for="Civic">
<input type="checkbox" id="Civic" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
Civic
</label>
<label for="Cadd">
<input type="checkbox" id="Cadd" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
Cadd
</label>
<label for="General">
<input type="checkbox" id="Cadd" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
General
</label>
'''
newtablehtml = ""
newtablehtmlheader = """<thead><tr>"""
newtablehtmlheader += "<th></th>"
newtablehtmlheader += "<th>Row Index</th>"
keys = {}
for key in list(list(nnewtable.values())[0].keys()):
keys[key] = {}
newtablehtmlbody = "<tbody>"
c = 0
keyc = 2
rowc = 0
addedkeys = []
popupdata = {}
for item1 in list(nnewtable.items()):
lenn = len(list(item1[1].items()))
print(lenn)
for subitem in zip(*item1[1].values()):
newtablehtmlbody += """<tr><td>
<br>
<button onclick="toggle(this)" style="color:white;font-size:20px;" name="+" class="btn btn-success btn-lg">
+
</button></td><td>%s</td>""" % item1[0]
for i in range(lenn):
mainKey = list(keys.keys())[i]
for item in list(subitem[i].items()):
val = item[1]
if type(val) == list and (type(val[0]) is OrderedDict or type(val[0]) is dict):
newtablehtmlbody += "<td>%s</td>" % (
getInnerAndHeaderHtmls(val,
"%s-%s-%s" % (item[0], rowc, c),
popupdata))
newtablehtmlheader += "<th>%s</th>" % item[0] if item[0] not in addedkeys else ""
if item[0] not in addedkeys:
keyc = addHeaderKeys(addedkeys, keys[mainKey], item[0], item[0], keyc)
elif type(val) == dict:
for key in val:
newtablehtmlbody += "<td>%s</td>" % (val[key])
newtablehtmlheader += "<th>%s</th>" % key if key not in addedkeys else ""
if key not in addedkeys:
keyc = addHeaderKeys(addedkeys, keys[mainKey], item[0], key, keyc, True)
else:
newtablehtmlbody += "<td>%s</td>" % (val)
newtablehtmlheader += "<th>%s</th>" % item[0] if item[0] not in addedkeys else ""
if item[0] not in addedkeys:
keyc = addHeaderKeys(addedkeys, keys[mainKey], item[0], item[0], keyc)
c += 1
newtablehtmlbody += "</tr>"
rowc += 1
c = 1
newtablehtmlheader += "</tr></thead>"
newtablehtmlbody += "</tbody>"
newtablehtml = """<table id = "table" class="table table-bordered">%s%s</table>""" % (
newtablehtmlheader, newtablehtmlbody)
return render_template("annotated.html", table=newtablehtml, mainKeys=mainKeys, subkeys=json.dumps(keys),
allData=nnewtable, popupdata=popupdata)
@app.route("/annotate", methods=["GET"])
def prevAnnotated():
if "table" in session:
nnewtable = session["table"].copy()
mainKeys = '''
<label for="Cosmic">
<input type="checkbox" id="Cosmic" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
Cosmic
</label>
<label for="Civic">
<input type="checkbox" id="Civic" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
Civic
</label>
<label for="Cadd">
<input type="checkbox" id="Cadd" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
Cadd
</label>
<label for="General">
<input type="checkbox" id="Cadd" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
General
</label>
'''
newtablehtml = ""
newtablehtmlheader = """<thead><tr>"""
newtablehtmlheader += "<th></th>"
newtablehtmlheader += "<th>Row Index</th>"
keys = {}
for key in list(list(nnewtable.values())[0].keys()):
keys[key] = {}
newtablehtmlbody = "<tbody>"
c = 0
keyc = 2
rowc = 0
addedkeys = []
popupdata = {}
for item1 in list(nnewtable.items()):
lenn = len(list(item1[1].items()))
print(lenn)
for subitem in zip(*item1[1].values()):
newtablehtmlbody += """<tr><td>
<br>
<button onclick="toggle(this)" style="color:white;font-size:20px;" name="+" class="btn btn-success btn-lg">
+
</button></td><td>%s</td>""" % item1[0]
for i in range(lenn):
mainKey = list(keys.keys())[i]
for item in list(subitem[i].items()):
val = item[1]
if type(val) == list and (type(val[0]) is OrderedDict or type(val[0]) is dict):
newtablehtmlbody += "<td>%s</td>" % (
getInnerAndHeaderHtmls(val,
"%s-%s-%s" % (item[0], rowc, c),
popupdata))
newtablehtmlheader += "<th>%s</th>" % item[0] if item[0] not in addedkeys else ""
if item[0] not in addedkeys:
keyc = addHeaderKeys(addedkeys, keys[mainKey], item[0], item[0], keyc)
elif type(val) == dict:
for key in val:
newtablehtmlbody += "<td>%s</td>" % (val[key])
newtablehtmlheader += "<th>%s</th>" % key if key not in addedkeys else ""
if key not in addedkeys:
keyc = addHeaderKeys(addedkeys, keys[mainKey], item[0], key, keyc, True)
else:
newtablehtmlbody += "<td>%s</td>" % (val)
newtablehtmlheader += "<th>%s</th>" % item[0] if item[0] not in addedkeys else ""
if item[0] not in addedkeys:
keyc = addHeaderKeys(addedkeys, keys[mainKey], item[0], item[0], keyc)
c += 1
newtablehtmlbody += "</tr>"
rowc += 1
c = 1
newtablehtmlheader += "</tr></thead>"
newtablehtmlbody += "</tbody>"
newtablehtml = """<table id = "table" class="table table-bordered">%s%s</table>""" % (
newtablehtmlheader, newtablehtmlbody)
return render_template("annotated.html", table=newtablehtml, mainKeys=mainKeys, subkeys=json.dumps(keys),
allData=nnewtable, popupdata=popupdata)
return redirect("/")
"""def getGenesFromLocation(chr, pos): # Gets location of gene, returns a Gene object (v102, v75, v54)
global data
gene = data.genes_at_locus(contig=chr, position=pos)
if not gene:
for db in dbs:
if db == session["dbChoice"]:
continue
data = EnsemblRelease(db)
chr, pos = mapping.remap(dbName[str(session["dbChoice"])], dbName[str(db)], chr, pos)
gene = data.genes_at_locus(contig=chr, position=pos)
if not gene:
continue
break
if not gene:
return Exception("Gene not found.")
return gene"""
"""def getGeneFromGeneId(gId): # Gets Ensembl id, returns a Gene object
global data
gene = data.gene_by_id(gId)
if not gene:
for db in dbs:
if db == session["dbChoice"]:
continue
data = EnsemblRelease(db)
gene = data.gene_by_id(gId)
if not gene:
continue
break
if not gene:
return Exception("Gene not found.")
return gene"""
def getGeneFromRsId(rsId): # Gets rsId, returns gene object
if session["dbChoice"] == 102:
varData = variant_client.getvariant(rsId, assembly="hg38")
if varData is None:
return Exception("Gene not found from rsId."), varData
elif session["dbChoice"] == 75:
varData = variant_client.getvariant(rsId, assembly="hg19")
if varData is None:
return Exception("Gene not found from rsId."), varData
else:
for assembly in ("hg19", "hg38"):
varData = variant_client.getvariant(rsId, assembly=assembly)
if varData is None:
continue
break
if varData is None:
return Exception("Gene not found from rsId."), varData
if type(varData) == dict:
if type(varData["cadd"]["gene"]) == list:
gene = getGeneFromGeneId(varData["cadd"]["gene"][0]["gene_id"])
else:
gene = getGeneFromGeneId(varData["cadd"]["gene"]["gene_id"])
elif type(varData) == list:
gene = getGeneFromGeneId(varData[1]["cadd"]["gene"][1]["gene_id"])
else:
return Exception("Unknown output format."), None
return gene, varData
@app.route("/getVariantData", methods=["GET"])
def getVariantsData():
gene = int(request.args.get("gene"))
variant = int(request.args.get("variant"))
variantType = str(request.args.get("type"))
if variantType != "civic" and variantType != "cosmic":
return Response(response=session["table"]["listofvariants"][gene][variant])
elif variantType == "civic":
return Response(response=session["table"]["listofvariantscivic"][gene][variant])
return Response(response=session["table"]["listofvariantscosmic"][gene][variant])
@app.route("/annotate/<rowid>", methods=["GET"])
def expression(rowid):
rowid = str(rowid)
# print(session["table"]["entrezgene"][rowid])
if "ncbi" in session["table"][rowid]["General"][0]["Entrezgene"]:
gene = session["table"][rowid]["General"][0]["Entrezgene"].split("href=\"")[1].split("\"")[0].split("/")[-1]
if requests.get(
"https://www.ncbi.nlm.nih.gov/projects/Gene/download_expression.cgi?PROJECT_DESC=PRJEB4337&GENE=%s" % gene).status_code == 500:
return render_template("visualization.html", table="", dta="[]")
data1 = requests.get(
"https://www.ncbi.nlm.nih.gov/projects/Gene/download_expression.cgi?PROJECT_DESC=PRJEB4337&GENE=%s" % gene).text
data1 = data1.split("\n\n\n")[1]
headers = data1.split("\n")[0].split("\t")
data1 = data1.split("\n")[1].split("\t")
tablehtml = '<table class="table table-bordered"><thead><tr>'
dta = []
for header, d in zip(headers, data1):
if header and header != "#GeneID":
dta.append({"name": str(header), "value": float(d)})
dta = sorted(dta, key=lambda i: i['value'])
for header in headers:
tablehtml += "<th>%s</th>" % header
tablehtml += "</tr></thead><tbody><tr>"
for d in data1:
tablehtml += "<td>%s</td>" % d
tablehtml += "</tr><tbody></table>"
return render_template("visualization.html", table=tablehtml, dta=json.dumps(dta))
return render_template("visualization.html", table="", dta="[]")
def processVariantData(variant, count, hgsvs, index):
variantdata = None
if str(variant["_id"]) in hgsvs:
variantdata = '<option value="%s-%s-%s">%s</option>' % (index, count, "biothings", variant["_id"])
observed = "observed" if variant["observed"] else "not observed"
varDict = {
"header": "Biothings: " + str(variant["_id"] + " (" + observed + ")")
}
for key in variant:
if variant[key] and key not in ["_id", "_version", "chrom", "hg19", "observed"]:
if type(variant[key]) != dict or all(isinstance(x, float) for x in list(variant[key].values())):
if len(list(variant[key].values())) > 2 and all(
isinstance(x, float) for x in list(variant[key].values())):
variant[key]["graph"] = """
<button onclick="showGraph('%s',this)">Show Graph</button>
""" % (key)
varDict[key] = json2html.convert(json=variant[key],escape=False)
elif type(variant[key]) == dict:
varDict[key] = {}
for key2 in variant[key]:
if type(variant[key][key2]) == dict and all(
isinstance(x, float) for x in list(variant[key][key2].values())):
variant[key][key2]["graph"] = """
<button onclick="showGraph('%s---%s',this)">Show Graph</button>
""" % (key2, key)
varDict[key][key2] = json2html.convert(json=variant[key][key2], escape=False)
varDict[key][key2] += "<div id='chart%s---%s'></div>" % (key2, key)
return json.dumps(varDict), variantdata
return None, None
def getVariantData(id, assembly, index, count, hgsvs, variantdata):
variant = variant_client.getvariant(id, assembly=assembly)
if type(variant) == dict and "_id" in variant:
vardict, vardata = processVariantData(variant, count, hgsvs, index)
if vardict:
variantdata += vardata
count += 1
elif type(variant) == list:
for var in variant:
if "_id" not in var:
continue
print(str(var["_id"]))
vardict, vardata = processVariantData(var, count, hgsvs, index)
if vardict:
variantdata += vardata
count += 1
return count, variantdata
def formatListOfLists(listofdicts):
for dictionary in listofdicts:
keys = list(dictionary.keys())
for key in keys:
if not dictionary[key]:
del dictionary[key]
return listofdicts
def formatDataForKeys(data, mainkeys, dictDescFunc):
for cs in data:
keys = list(cs.keys())
for key in keys:
if key not in mainkeys:
del cs[key]
else:
data = cs[key]
if "http" in data:
data = '<a target="_blank" href="%s">%s</a>' % (data,data)
cs[dictDescFunc(key)] = data
del cs[key]
def processVCFRecord(record, index, nnewtable, value):
mappedChr, mappedPos = mapping.remap(dbName[str(session["dbChoice"])], "GRCh37", record.CHROM, record.POS)
foundGene = False
gene_dict = {}
main_sub_dict = {
index: {
"General": [],
"Civic": [],
"Cosmic": [],
"Cadd": [],
}
}
try:
civic_variants_template = {}
for key in dictKeys.civicVariants:
civic_variants_template[dictKeys.civicDesc(key)] = ""
cosmic_CMC_template = {}
for key in dictKeys.cosmicCMC:
cosmic_CMC_template[dictKeys.cosmicDesc(key)] = ""
except:
traceback.print_exc()
return
if record.ALT:
for i in record.ALT:
main_sub_dict[index]["General"].append({
"Chromosome":str(record.CHROM),
"Position":str(record.POS),
"Reference Bases":str(record.REF),
"Alternative Bases":str(i),
"Summary": "",
"Entrezgene": "",
"Strand": "",
"Gene Start": "",
"Gene End": "",
"Gene Type": "",
"Gene Name": "",
"Variant Type": "",
"Expression": "",
"Gene Description":"",
"Clingen": "",
"Gene Id":"",
})
if record.ID and "rs" in record.ID: # RsId exists
# print("rsid exists")
try:
gene, variant = getGeneFromRsId(record.ID)
gene_dict = gene.__dict__
foundGene = True
cnt = 0
if record.ALT:
for i in record.ALT:
getGeneInfo(gene_dict["id"], main_sub_dict[index]["General"][cnt])
for key in gene_dict.keys():
if key in list(main_sub_dict[index]["General"][cnt].keys()) or key in ensembl_keys:
if key in ensembl_keys:
if key == "id":
main_sub_dict[index]["General"][cnt][ensembl_keys[key]] = "<a target=\"_blank\" href=\"https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=%s\">%s</a>" % (str(gene_dict[key]),str(gene_dict[key]))
else:
main_sub_dict[index]["General"][cnt][ensembl_keys[key]] = str(gene_dict[key])
else:
main_sub_dict[index]["General"][cnt][key.replace("_"," ")] = str(gene_dict[key])
main_sub_dict[index]["General"][cnt]["Expression"] = '<a target=\"_blank\" href="/annotate/%s">Expression Graph</a>' % (index)
cnt += 1
except Exception as e:
print("getGeneFromRsId: ", e)
foundGene = False
if not foundGene:
# if not record.ID: print("rsid does not exist")
try:
gene = getGenesFromLocation(record.CHROM, record.POS, session["dbChoice"])
gene_dict = gene[0].__dict__
foundGene = True
cnt = 0
if record.ALT:
for i in record.ALT:
getGeneInfo(gene_dict["id"], main_sub_dict[index]["General"][cnt])
for key in gene_dict.keys():
if key in list(main_sub_dict[index]["General"][cnt].keys()) or key in ensembl_keys:
if key in ensembl_keys:
if key == "id":
main_sub_dict[index]["General"][cnt][ensembl_keys[key]] = "<a target=\"_blank\" href=\"https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=%s\">%s</a>" % (str(gene_dict[key]),str(gene_dict[key]))
else:
main_sub_dict[index]["General"][cnt][ensembl_keys[key]] = str(gene_dict[key])
else:
main_sub_dict[index]["General"][cnt][key.replace("_"," ")] = str(gene_dict[key])
main_sub_dict[index]["General"][cnt]["Expression"] = '<a target=\"_blank\" href="/annotate/%s">Expression Graph</a>' % (index)
cnt += 1
except Exception as e:
print("getGenesFromLocation: ", e)
foundGene = False
try:
count = 0
mappedChr, mappedPos = mapping.remap(dbName[str(session["dbChoice"])], "GRCh37", record.CHROM, record.POS)
variantdata = ""
hgsvs = []
except:
print(traceback.format_exc())
try:
if record.ALT:
for i in record.ALT:
hgsvs.append(str(variant_client.format_hgvs(mappedChr, mappedPos, record.REF, str(i))))
except:
print(traceback.format_exc())
try:
cnt = 0
if record.ALT:
for i in record.ALT:
if len(str(i)) == 1 and len(str(record.REF)) == 1:
cadd_data = cadd.getSNV("GRCh37", mappedChr, mappedPos, record.REF, str(i))
if cadd_data and type(cadd_data) == list:
d = cadd_data[0]
cadd_dict = {}
for key in cadd.keys:
if d[key] == "NA":
d[key] = ""
if key in d:
cadd_dict[key.replace("-", " ").replace("_", " ")] = d[key]
else:
cadd_dict[key] = ""
main_sub_dict[index]["Cadd"].append(cadd_dict)
else:
temp1 = {}
for key2 in cadd.keys:
temp1[key2] = ""
main_sub_dict[index]["Cadd"].append(temp1)
else:
temp1 = {}
for key2 in cadd.keys:
temp1[key2] = ""
main_sub_dict[index]["Cadd"].append(temp1)
except:
print(traceback.format_exc())
try:
if record.ID:
count, variantdata = getVariantData(record.ID, biothingsAssembly, index, count, hgsvs,
variantdata)
elif hgsvs:
for hgsv in hgsvs:
count, variantdata = getVariantData(hgsv, biothingsAssembly, index, count, hgsvs,
variantdata)
except:
print(traceback.format_exc())
try:
cnt = 0
if record.ALT:
for i in record.ALT:
civicdata = civic.findVariantsFromLocation(mappedChr, mappedPos, str(record.REF), str(i)).copy()
print("civic len",len(civicdata))
if civicdata:
count = 0
for var in [civicdata[0]]:
variant_groups = formatListOfLists(civic.findVariantGroups(var["variant_groups"])).copy()
assertions = formatListOfLists(civic.findAssertions(var["variant_id"])).copy()
clinical_significances = formatListOfLists(
civic.findClinicalEvidences(var["variant_id"])).copy()
civicdatagene = civic.findGeneFromLocation(mappedChr, mappedPos).copy()
civicdatagene = formatListOfLists([civicdatagene])
formatDataForKeys(clinical_significances, dictKeys.civicClinicalEvidences, dictKeys.civicDesc)
formatDataForKeys(assertions, dictKeys.civicAssertions, dictKeys.civicDesc)
formatDataForKeys(variant_groups, dictKeys.civicVariantGroups, dictKeys.civicDesc)
formatDataForKeys(civicdatagene, dictKeys.civicGenes, dictKeys.civicDesc)
genehtml = civicdatagene
keys = list(var.keys())
for key in keys:
if key in ["variant"]:
continue
if key not in dictKeys.civicVariants:
del var[key]
continue
data = var[key]
if "http" in data:
data = '<a target="_blank" href="%s">%s</a>' % (data,data)
var[dictKeys.civicDesc(key)] = data
del var[key]
temp = {}
for key in list(civic_variants_template.keys()):
temp[key] = var[key]
var = temp.copy()
html = var
CivicDict = {
"Variants": html if html else civic_variants_template,
"Variant Groups": variant_groups if variant_groups else "",
"Genes": genehtml if genehtml else "",
"Assertions": assertions if assertions else "",
"Clinical Evidences": clinical_significances if clinical_significances else "",
}
main_sub_dict[index]["Civic"].append(CivicDict)
count += 1
else:
main_sub_dict[index]["Civic"].append(
{
"Variants": civic_variants_template,
"Variant Groups": "",
"Genes": "",
"Assertions": "",
"Clinical Evidences": "",
}
)
main_sub_dict[index]["General"][cnt]["Alternative Bases"] = str(i)
cnt += 1
except:
print(traceback.format_exc())
try:
cnt = 0
if record.ALT:
for i in record.ALT:
lastdb = 75
cosmicdata = cosmic.findVariantsFromLocation("GRCh37", mappedChr, mappedPos, str(record.REF), str(i))
if not cosmicdata:
mappedChr, mappedPos = mapping.remap(dbName[str(session["dbChoice"])], "GRCh38", record.CHROM,
record.POS)
cosmicdata = cosmic.findVariantsFromLocation("GRCh38", mappedChr, mappedPos, str(record.REF), str(i))
lastdb = 102
if cosmicdata:
count = 0
for row in [cosmicdata[0]]:
if "legacy_mutation_id" in row and row["legacy_mutation_id"]:
resistanceMutations = cosmic.findResistanceMutations(row["legacy_mutation_id"])
for res in resistanceMutations:
reskeys = list(res.keys())
for key in reskeys:
if key not in dictKeys.cosmicResistanceMutations:
del res[key]
else:
res[dictKeys.cosmicDesc(key)] = res[key]
del res[key]
row["legacy_mutation_id"] = "<a target=\"_blank\" href=\"https://cancer.sanger.ac.uk/cosmic/search?q=%s\">%s</a>" % (row["legacy_mutation_id"],row["legacy_mutation_id"])
keys = list(row.keys())
for key in keys:
if key in ensembl_keys:
if row[key]:
main_sub_dict[index]["General"][cnt][ensembl_keys[key]] = row[key]
else:
data = getVariantFromLocation(mappedChr,mappedPos,str(record.REF),str(i),lastdb)
if data:
print(data.keys())
for key in data:
if key in ensembl_keys and ensembl_keys[key] == "Variant Type":
main_sub_dict[index]["General"][cnt][ensembl_keys[key]] = data[key]
break
if (key not in dictKeys.cosmicCMC):
del row[key]
elif not row[key]:
row[key] = ""
else:
row[dictKeys.cosmicDesc(key)] = row[key]
del row[key]
temp = {}
for key in list(cosmic_CMC_template.keys()):
if key in row:
temp[key] = row[key]
else:
temp[key] = ""
row = temp
variantData = json2html.convert(json=row, escape=False)
variantData = row
CosmicDict = {
"CMC": variantData if variantData else cosmic_CMC_template,
"Resistance Mutations": resistanceMutations if resistanceMutations else ""
}
main_sub_dict[index]["Cosmic"].append(CosmicDict)
count += 1
else:
data = getVariantFromLocation(mappedChr,mappedPos,str(record.REF),str(i),lastdb)
if data:
for key in data:
if key in ensembl_keys and ensembl_keys[key] == "Variant Type":
print("Ensembl",data[key])
main_sub_dict[index]["General"][cnt][ensembl_keys[key]] = data[key]
break
main_sub_dict[index]["Cosmic"].append(
{
"CMC": cosmic_CMC_template,
"Resistance Mutations": ""
}
)
main_sub_dict[index]["General"][cnt]["Alternative Bases"] = str(i)
cnt += 1
except Exception as exp:
print(index, "- variant exp: ", exp)
print(traceback.format_exc())
try:
greatest_len = 0
for key in ["Cosmic", "Civic", "Cadd", "General"]:
if len(main_sub_dict[index][key]) > greatest_len:
greatest_len = len(main_sub_dict[index][key])
for key in ["Cosmic", "Civic", "Cadd", "General"]:
while greatest_len > len(main_sub_dict[index][key]):
if key == "Cosmic":
main_sub_dict[index][key].append(
{
"CMC": cosmic_CMC_template,
"Resistance Mutations": ""
}
)
elif key == "Cadd":
temp1 = {}
for key2 in cadd.keys:
temp1[key2] = ""
main_sub_dict[index][key].append(temp1)
elif key == "Civic":
main_sub_dict[index][key].append(
{
"Variants": civic_variants_template,
"Variant Groups": "",
"Genes": "",
"Assertions": "",
"Clinical Evidences": "",
}
)
else:
main_sub_dict[index][key].append({
"Chromosome":str(record.CHROM),
"Position":str(record.POS),
"Reference Bases":str(record.REF),
"Alternative Bases":str(record.ALT),
"Summary": "",
"Entrezgene": "",
"Strand": "",
"Gene Start": "",
"Gene End": "",
"Gene Type": "",
"Gene Name": "",
"Variant Type": "",
"Expression": "",
"Gene Description":"",
"Clingen": "",
"Gene Id":"",
})
except:
print(traceback.format_exc())
if greatest_len > 0:
nnewtable[str(index)] = {
"General": main_sub_dict[index]["General"],
"Civic": main_sub_dict[index]["Civic"],
"Cosmic": main_sub_dict[index]["Cosmic"],
"Cadd": main_sub_dict[index]["Cadd"],
}
value.value = value.value + 1
@app.route("/showresult", methods=["GET"])
def showresult():
global tempSession
try:
print("processed rows: " , tempSession[str(session["stamp"]) + "count"] , ", time elapsed (seconds): " , time.time()-session["stamp"])
except:
print("time exception")
if "stamp" in session and session["stamp"] in tempSession:
try:
(newtablehtml, mainKeys, keys, nnewtable, popupdata) = tempSession[session["stamp"]]
session["result"] = tempSession[session["stamp"]]
session["table"] = nnewtable.copy()
return render_template("annotated.html", table=newtablehtml, mainKeys=mainKeys, subkeys=json.dumps(keys),
allData=nnewtable, popupdata=popupdata)
except:
if "result" in session:
(newtablehtml, mainKeys, keys, nnewtable, popupdata) = session["result"]
session["table"] = nnewtable.copy()
return render_template("annotated.html", table=newtablehtml, mainKeys=mainKeys,
subkeys=json.dumps(keys), allData=nnewtable, popupdata=popupdata)
else:
print("exception")
return redirect("/annotate")
elif "result" in session:
(newtablehtml, mainKeys, keys, nnewtable, popupdata) = session["result"]
session["table"] = nnewtable.copy()
return render_template("annotated.html", table=newtablehtml, mainKeys=mainKeys, subkeys=json.dumps(keys),
allData=nnewtable, popupdata=popupdata)
print("lastresult")
return redirect("/annotate")
@app.route("/isresult", methods=['GET'])
def isresult():
print(session.keys())
progress = 0
rowsprocessed = 0
try:
if "stamp" in session and session["stamp"] in tempSession:
session["result"] = tempSession[session["stamp"]]
session["done"] = "done"
return Response(response=json.dumps({"status": 1}))
except:
if "table" in session:
return Response(response=json.dumps({"status": 1}))
if "stamp" in session:
if str(session["stamp"]) + "progress" in tempSession and str(session["stamp"]) + "count" in tempSession:
progress = tempSession[str(session["stamp"]) + "progress"].value / tempSession[
str(session["stamp"]) + "count"] * 100
rowsprocessed = tempSession[str(session["stamp"]) + "progress"].value
return Response(response=json.dumps({
"status": 0,
"progress": progress,
"rowsprocessed":rowsprocessed
}))
def addHeaderKeys(addedkeys, civickeys, itemkey, key, keycount, isdict=False):
addedkeys.append(key)
if isdict:
if itemkey not in civickeys:
civickeys[itemkey] = {}
civickeys[itemkey][key] = keycount
else:
civickeys[itemkey] = keycount
return keycount + 1
def getInnerAndHeaderHtmls(elements, key, popupdata):
innerhtml = "<option value="" selected>""</option>"
for element in elements:
header = list(element.values())[0]
if "CIViC: Disease" in element:
header = element["CIViC: Disease"]
if "disease_label" in element:
header = element["disease_label"]
if "http" in header:
header = header.split("</")[0].split(">")[1]
innerhtml += """
<option value="%s|%s">%s</option>
""" % (key, header, header)
popupdata[key + "|" + header] = json2html.convert(json=element,escape=False)
innerhtmlselect = """<select onchange="toggleModal(this)">%s</select>
""" % (innerhtml)
return innerhtmlselect
@app.route("/haveaprocess", methods=["GET"])
def haveaprocess():
if "stamp" in session:
return Response(response=json.dumps({"status": 1}))
return Response(response=json.dumps({"status": 0}))
@app.route("/annotate", methods=["POST"])
def annotate():
try:
global tempSession
stamp = time.time()
if "stamp" in session:
if session["stamp"] in tempSession:
del tempSession[session["stamp"]]
del session["stamp"]
if "table" in session:
print("table in")
del session["table"]
if "result" in session:
print("result deleted")
del session["result"]
session["stamp"] = stamp
start = time.time()
print(request.form["db"])
session["dbChoice"] = int(request.form["db"])
print("DB choice:", session["dbChoice"])
global data
# data = EnsemblRelease(session["dbChoice"])
records = []
file = request.files["efile"]
file.name = file.filename
file = BufferedReader(file)
file = TextIOWrapper(file)
tempSession[str(stamp) + "progress"] = 0
vcf_reader = vcf.Reader(file)
count = 0
for record in vcf_reader:
records.append(record)
count += 1
tempSession[str(stamp) + "count"] = count
# print(type(file))
@copy_current_request_context
def annotatefunc(records, stamp):
try:
global tempSession
mainKeys = '''
<label for="Cosmic">
<input type="checkbox" id="Cosmic" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
Cosmic
</label>
<label for="Civic">
<input type="checkbox" id="Civic" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
Civic
</label>
<label for="Cadd">
<input type="checkbox" id="Cadd" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
Cadd
</label>
<label for="General">
<input type="checkbox" id="General" onclick="changeSelectText(this.parentElement)" onchange="resetSubkeys(this.parentElement,this)" />
General
</label>
'''
newtable = manager.dict()
tempSession[str(stamp) + "progress"] = manager.Value('progress', 0)
nnewtable = {}
pool = Pool(os.cpu_count())
count = 0
for record in records:
pool.apply_async(processVCFRecord, (record, count, newtable, tempSession[str(stamp) + "progress"]))