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