Add all the source codes into the github.

1 files changed, 107 insertions, 0 deletions

diff --git a/web/webqtl/maintainance/addRif.py b/web/webqtl/maintainance/addRif.py
new file mode 100755
index 00000000..c7cdde7a
--- /dev/null
+++ b/web/webqtl/maintainance/addRif.py
@@ -0,0 +1,107 @@
+# 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()