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Util.py
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Util.py
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"""Utility functionality used across multiple controllers"""
# from google.appengine.ext import webapp
import webapp2
from jinja2 import Environment, FileSystemLoader
import os
import simplejson
import logging
from google.appengine.ext import db
from google.appengine.api import memcache, users, search
from datetime import datetime
from models.users import UserData
from models.study import Study, GWAS, Gene, Snp, Disease
from Bio import Entrez
import StringIO
import csv
from google.appengine.api import memcache
def reset():
"""resets the mem-cache:
(auto-reset on deploy)[http://stackoverflow.com/questions/1983556/how-can-i-have-google-app-engine-clear-memcache-every-time-a-site-is-deployed]
"""
memcache.flush_all()
def AddStudyDocument(study):
doc = search.Document(doc_id=study.pubmed_id, # Treat pubmed_id as key
fields=[
search.TextField(name='name', value=study.name),
search.TextField(name='disease_trait', value=study.disease_trait),
search.TextField(name='abstract', value=study.abstract)
])
search.Index(name=study._index).add(doc)
def AddSNPDocument(snp):
doc = search.Document(
fields=[
search.TextField(name='snpid', value=snp.snpid),
])
search.Index(name=snp._index).add(doc)
def AddGeneDocument(gene):
doc = search.Document(doc_id=gene.geneid,
fields=[
search.TextField(name='name', value=gene.name),
search.TextField(name='alias', value=str(gene.alias)),
])
search.Index(name=gene._index).add(doc)
def populate(path="gwascatalog.txt", limit=200):
"""Populate the database with data from gwascatalog.txt"""
docs = csv.DictReader(open(path,'rb'), dialect='excel-tab')
pubids = {}
for doc in docs:
pubid = doc["PUBMEDID"]
if pubids.has_key(pubid):
pubids[pubid].append(doc)
else:
pubids[pubid] = [doc]
i = 0
for pid, line in pubids.iteritems():
i += 1
if i == limit:
break
rel = line[0]
# print pid
disease_name = rel["Disease/Trait"].strip().lower()
disease = Disease.get_or_insert(disease_name,
name=disease_name)
study = Study.get_or_insert(pid,
name=rel["Study"],
disease_trait = disease_name,
disease_ref = disease,
pubmed_id = pid)
# print rel["Date"].strip()
date = datetime.strptime(rel["Date"].strip(), "%m/%d/%Y").date()
# print date
study.date = date
study.pubmed_url=rel["Link"].strip()
study.init_sample = rel["Initial Sample Size"].strip()
study.repl_sample= rel["Replication Sample Size"].strip()
study.platform = rel["Platform [SNPs passing QC]"].strip()
study.put()
AddStudyDocument(study)
for rel in line:
# init gene relation
gene = None
up_gene = None
down_gene = None
# if intergenic gwas, we go nuts..
intergenic = rel["Intergenic"] == "2"
if not intergenic:
geneid = rel["Snp_gene_ids"].strip()
if geneid != "":
# not intergenic => one direct gene
names = rel["Mapped_gene"].split(" - ")
if len(names) == 1:
gene = Gene.get_or_insert(geneid,
name = rel["Mapped_gene"],
geneid = geneid)
if not study.key() in gene.studies:
gene.studies.append(study.key())
if not disease.key() in gene.diseases:
gene.diseases.append(disease.key())
gene.put()
AddGeneDocument(gene)
else:
# up and downstream genes must be set
down_id = rel["Downstream_gene_id"].strip()
up_id = rel["Upstream_gene_id"].strip()
if up_id != "" and down_id != "":
up_down_names = rel["Mapped_gene"].split(" - ")
if len(up_down_names) < 2:
# gene = NR / NS or whatever..
up_down_names = ["N/A", "N/A"]
# create upstream gene
up_name = up_down_names[0]
down_name = up_down_names[1]
# print down_name, up_name
# assert("-" not in up_name)
# assert("-" not in down_name)
assert(up_id != "")
assert(down_id != "")
up_gene = Gene.get_or_insert(up_id,
name = up_name,
geneid = up_id)
# up_gene.study.append(study.key())
down_gene = Gene.get_or_insert(down_id,
name = down_name,
geneid = down_id)
# up_gene.study.append(study.key())
# init snps..
snp = None
snpid = rel["Snp_id_current"].strip()
if snpid != "":
# non=blank snp
try:
# create relation only if a 'single' snp is in the gwas
int(snpid)
snp = Snp.get_or_insert(snpid,
snpid=snpid)
if gene:
snp.gene = gene
if not study.key() in snp.studies:
snp.studies.append(study.key())
if not disease.key() in snp.diseases:
snp.diseases.append(disease.key())
snp.put()
AddSnpDocument(snp)
except:
# haplotype?
snpid = "N/A"
# if no gene or snp relation is mentioned - ignore and just insert study
if (gene is None or up_gene is None) and snp is None:
print "skipping gwas"
continue
# init gwas
gwas = GWAS(study=study, intergenic=intergenic, disease=disease)
if intergenic:
if down_gene is not None and up_gene is not None:
gwas.downstream = down_gene
gwas.upstream = up_gene
else:
# could be None
gwas.gene = gene
# parse remaining gwas information
gwas.p_string = rel["p-Value"].strip()
# could be none
gwas.snps = snpid
# parse out the exponent: 6E-8 => -8
try:
# test that p-Value is actually a float before parsing out
float(rel["p-Value"])
gwas.p_val = int(rel["p-Value"].split("E")[1])
except Exception, e:
# print e
# forces the filter to downgrade this gwas wrt. p-value
gwas.p_val = 0
# could be interesting
gwas.strongest_snp_risk_allele = \
rel["Strongest SNP-Risk Allele"].strip()
# gwas.CI = rel["95% CI (text)"].strip()
gwas.OR_beta = rel["OR or beta"].strip()
gwas.riscAlleleFrequency = \
rel["Risk Allele Frequency"].strip()
gwas.put()
memcache.delete('gwas_main')
print "done"
def purge():
"""Clear the database to make ready for (re-)population"""
for model in ["Snp", "Gene", "GWAS", "Study", "Disease"]:
try:
while True:
q = db.GqlQuery("SELECT __key__ FROM %s" % model)
assert q.count()
db.delete(q.fetch(200))
except Exception, e:
print e
pass
print "done"
def snp_omim(snpids=None):
"""given list of snpids - returns the list of related OMIM IDs"""
if not snpids:
return []
handle = Entrez.elink(db="omim", dbfrom="snp", id=snpids,linkname="snp_omim")
from_dbs = Entrez.read(handle)
handle.close()
omim_ids = [] # holds the id of each of the referened articles
# for each database with references to this snp
for from_db in from_dbs:
# print db
if not from_db.has_key("LinkSetDb"):
continue
# print db
for to_db in from_db["LinkSetDb"]:
for link in to_db["Link"]:
omim_ids.append(link['Id'])
return omim_ids
def omim_efetch(db=None, ids=None):
"""Omin fetch"""
handle = Entrez.efetch(db=db, id=ids, retmode="xml")
pubs = Entrez.read(handle)
handle.close()
print pubs
class jTemplate():
"""Template helper, sets the template base path and uses a given renderer on
the template."""
_e = Environment(loader=FileSystemLoader(os.path.join(
os.path.dirname(__file__), 'templates')))
@staticmethod
def render(template, variables, printer):
t = jTemplate._e.get_template(template)
printer(t.render(variables))
env = Environment(loader=FileSystemLoader(os.path.join(
os.path.dirname(__file__), 'templates')))
class AppRequestHandler(webapp2.RequestHandler):
"""Base class for controllers"""
_template = None
def render(self, template = None, **args):
if template is None:
raise Exception("No 'template' argument to render from")
temp = env.get_template(template)
return temp.render(**args)
def setTemplate(self, template):
"""Set the template to be used for calls rendering"""
self._template = template
def out(self, **dictionary):
"""Render the template, passing a dict as inputs"""
if self._template is None:
# Get template from controller / method names
actionName = self.__class__.__name__
self._template = actionName+".html"
dictionary['user'] = UserData.current()
dictionary['user_logout'] = users.create_logout_url('/')
dictionary['user_login'] = users.create_login_url('/')
dictionary['user_admin'] = users.is_current_user_admin()
temp = env.get_template(self._template)
self.response.write(temp.render(dictionary))
def toJson(self, dictionary, prettify = False):
"""Display JSON data template.
Prettify flag tells whether to use the google code prettify markup"""
enc = simplejson.JSONEncoder()
data = {"json": enc.encode(dictionary)}
if prettify:
jTemplate.render("data/prettify/json.html", data , self.response.out.write);
else:
jTemplate.render("data/json.html", data , self.response.out.write);
def toXML(self, xml, prettify = False):
"""Display XML data template.
Prettify flag tells whether to use the google code prettify markup"""
data = {'xml':xml}
if prettify:
jTemplate.render("data/prettify/xml.html", data, self.response.out.write);
else:
jTemplate.render("data/xml.html", data,self.response.out.write );