from bioservices import ChEMBL, QuickGO, Reactome, KEGG
from py2neo import Graph
from model.core import *
from ncbi import fetch_publication_list
from quickgo import fetch_quick_go_data
from uniprot import *
graph = Graph(host=os.environ.get("DB", "localhost"),
bolt=True,
password=os.environ.get("NEO4J_PASSWORD", ""))
chembl = ChEMBL(verbose=False)
quick_go = QuickGO(verbose=False)
reactome = Reactome(verbose=False)
kegg = KEGG(verbose=False)
# watch("neo4j.bolt")
gene_dict = dict()
transcript_dict = dict()
pseudogene_dict = dict()
cds_dict = dict()
exon_dict = dict()
rrna_dict = dict()
trna_dict = dict()
ncrna_dict = dict()
location_dict = dict()
go_term_set = set()
def reactome():
return Reactome(verbose=True)
spamwriter = csv.writer(csvfile,
delimiter=',',
quotechar='|',
quoting=csv.QUOTE_MINIMAL)
spamwriter.writerow(['GENE', 'HITS'])
for gene in gene_dict.keys():
nop = len(gene_dict[gene])
print 'Gene code: ' + gene
print 'Number of pathways: ' + str(nop)
spamwriter.writerow([str(gene), str(nop)])
for pathway in gene_dict[gene]:
print human_pathways_dict[pathway]
print '\n'
print "!! REACTOME !!"
react = Reactome()
#"Currently only human pathways will be returned from this method"
with open('REACTOME_stats.csv', 'wb') as csvfile:
spamwriter = csv.writer(csvfile,
delimiter=',',
quotechar='|',
quoting=csv.QUOTE_MINIMAL)
spamwriter.writerow(['GENE', 'HITS'])
for gene in gene_list:
pathway_list = react.query_hit_pathways(gene)
nop = len(pathway_list)
spamwriter.writerow([str(gene), str(nop)])
for p in pathway_list:
print gene + ': ' + p["displayName"] + ' , ' + p[
"stableIdentifier"]["displayName"]
def get_species_name_to_id():
r = Reactome()
species_name_to_id = {x['displayName']: x['dbId'] for x in r.data_species_all()}
return species_name_to_id
Options:
-h --help Show help.
--version Show version.
"""
import os
import requests
from lxml import etree
import json
from bioservices import Reactome
import logging
log = logging.getLogger('root')
s = Reactome()
wsUrl = 'http://reactome.org/ReactomeRESTfulAPI/RESTfulWS' # base Url for Reactome Webservice
def getEntityData(dbId, downloadDir=None):
''' Get reactome entities by database id'''
if not downloadDir:
downloadDir = './downloadedEntities'
fn = '{}/{}.json'.format(downloadDir, dbId)
if os.path.isfile(fn):
with open(fn, 'r') as f:
entity = json.load(f)
print "!! KEGG !!"
with open('KEGG_stats.csv', 'wb') as csvfile:
spamwriter = csv.writer(csvfile, delimiter=',', quotechar='|', quoting=csv.QUOTE_MINIMAL)
spamwriter.writerow(['GENE', 'HITS'])
for gene in gene_dict.keys():
nop = len(gene_dict[gene])
print 'Gene code: ' + gene
print 'Number of pathways: ' + str(nop)
spamwriter.writerow([str(gene), str(nop)])
for pathway in gene_dict[gene]:
print human_pathways_dict[pathway]
print '\n'
print "!! REACTOME !!"
react = Reactome()
#"Currently only human pathways will be returned from this method"
with open('REACTOME_stats.csv', 'wb') as csvfile:
spamwriter = csv.writer(csvfile, delimiter=',', quotechar='|', quoting=csv.QUOTE_MINIMAL)
spamwriter.writerow(['GENE', 'HITS'])
for gene in gene_list:
pathway_list = react.query_hit_pathways(gene)
nop = len(pathway_list)
spamwriter.writerow([str(gene), str(nop)])
for p in pathway_list:
print gene +': '+ p["displayName"] +' , '+ p["stableIdentifier"]["displayName"]
def setup_class(klass):
klass.e = Reactome(verbose=True)