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Diffstat (limited to 'scripts/addRif')
| -rwxr-xr-x | scripts/addRif | 129 |
1 files changed, 0 insertions, 129 deletions
diff --git a/scripts/addRif b/scripts/addRif deleted file mode 100755 index 4d33af3..0000000 --- a/scripts/addRif +++ /dev/null @@ -1,129 +0,0 @@ -# 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 os -import sys -import MySQLdb - -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") |