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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by Lei Yan 2011/02/08
# created by Lei Yan 02/08/2011
import string
import MySQLdb
import time
import os
import sys
path1 = os.path.abspath(os.path.dirname(__file__))
path2 = path1 + "/.."
path3 = path1 + "/../../tmp"
sys.path.insert(0, path2)
from base import webqtlConfig
try:
con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER,passwd=webqtlConfig.DB_PASSWD)
cursor = con.cursor()
print "You have successfully connected to mysql.\n"
except:
print "You entered incorrect password.\n"
sys.exit(0)
taxIds = {'10090':1, '9606':4, '10116':2, '3702':3}
taxIdKeys = taxIds.keys()
os.chdir(path3)
cdict = {}
os.system("rm -f gene_info")
os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz")
os.system("gunzip gene_info.gz")
try:
fp = open("gene_info")
except:
print "gene_info doesn't exit"
sys.exit(1)
i=0
line = fp.readline()
while line:
line2 = map(string.strip, string.split(line.strip(), "\t"))
if line2[0] in taxIdKeys:
cdict[line2[1]] = line2[2]
line = fp.readline()
i += 1
if i%1000 == 0:
print "finished ", i
fp.close()
os.system("rm -f generifs_basic")
os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/GeneRIF/generifs_basic.gz")
os.system("gunzip generifs_basic.gz")
try:
fp = open("generifs_basic")
except:
print "generifs_basic doesn't exist"
sys.exit(1)
cursor.execute("delete from GeneRIF_BASIC")
count = 0
line = fp.readline()
while line:
line2 = map(string.strip, string.split(line.strip(), "\t"))
if line2[0] in taxIdKeys:
count += 1
line2[0] = taxIds[line2[0]]
if len(line2) !=5:
print line
else:
try:
symbol=cdict[line2[1]]
except:
symbol= ""
line2 = line2[:2] + [symbol] + line2[2:]
cursor.execute("insert into GeneRIF_BASIC(SpeciesId, GeneId, Symbol, PubMed_ID, createtime, comment) values(%s, %s, %s, %s, %s, %s)", tuple(line2))
line = fp.readline()
fp.close()
print count, "\n"
cursor.close()
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