feat: copy addRif script from genenetwork1

original: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/maintainance/addRif.py
Included some changes to make it python3 compatible

1 files changed, 126 insertions, 0 deletions

diff --git a/scripts/addRif.py b/scripts/addRif.py
new file mode 100755
index 0000000..8ea5f74
--- /dev/null
+++ b/scripts/addRif.py
@@ -0,0 +1,126 @@
+# 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)
+
+def fetchrif():
+	try:
+		con = MySQLdb.Connect(db="gn3", host="localhost", user="gn2", passwd="password")
+		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)
+	print("path3: %s" % (path3))
+	genedict = {}
+
+	os.system("rm -vf gene_info")
+	os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz")
+	os.system("gunzip gene_info.gz")
+
+	file = open("gene_info", 'r')
+	i = 0
+	for line1 in file:
+		line1 = line1.strip()
+		if line1.startswith('#'):
+			continue
+		line2 = line1.strip().split("\t")
+		if line2[0] in taxIdKeys:
+			genedict[line2[1]] = line2[2]
+		i += 1
+		if i%1000000 == 0:
+			print("finished: %d" % (i))
+	print("finished all: %d" % (i))
+	file.close()
+
+	os.system("rm -vf generifs_basic")
+	os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/GeneRIF/generifs_basic.gz")
+	os.system("gunzip generifs_basic.gz")
+
+	file = open("generifs_basic", 'r')
+	i = 0
+	for line1 in file:
+		line1 = line1.strip()
+		if line1.startswith('#'):
+			continue
+		line2 = line1.strip().split("\t")
+		if line2[0] in taxIdKeys and len(line2) >= 5:
+			line2[0] = taxIds[line2[0]]
+			try:
+				symbol = genedict[line2[1]]
+			except:
+				symbol = ""
+			sql = """
+				SELECT COUNT(*)
+				FROM GeneRIF_BASIC
+				WHERE GeneRIF_BASIC.`SpeciesId`=%s
+				AND GeneRIF_BASIC.`GeneId`=%s
+				AND GeneRIF_BASIC.`PubMed_ID`=%s
+				AND GeneRIF_BASIC.`createtime`=%s
+				AND GeneRIF_BASIC.`comment`=%s
+				"""
+			cursor.execute(sql, (line2[0], line2[1], line2[2], line2[3], line2[4]))
+			c = cursor.fetchone()[0]
+			if c == 0:
+				print("to insert...")
+				sql = """
+					INSERT INTO GeneRIF_BASIC
+					SET GeneRIF_BASIC.`SpeciesId`=%s,
+						GeneRIF_BASIC.`GeneId`=%s,
+						GeneRIF_BASIC.`symbol`=%s,
+						GeneRIF_BASIC.`PubMed_ID`=%s,
+						GeneRIF_BASIC.`createtime`=%s,
+						GeneRIF_BASIC.`comment`=%s
+					"""
+				cursor.execute(sql, (line2[0], line2[1], symbol, line2[2], line2[3], line2[4]))
+		i += 1
+		if i%100000 == 0:
+			print("finished: %d" % (i))
+	print("finished all: %d" % (i))
+	file.close()
+	cursor.close()
+# /usr/bin/python addRif.py
+
+if __name__ == "__main__":
+	print("command line arguments:\n\t%s" % sys.argv)
+	fetchrif()
+	print("exit successfully")