1 files changed, 0 insertions, 170 deletions
diff --git a/web/genotypes/process.py b/web/genotypes/process.py
deleted file mode 100755
index 96cbc9b4..00000000
--- a/web/genotypes/process.py
+++ /dev/null
@@ -1,170 +0,0 @@
-#!/usr/bin/python
-import sys
-import os
-import string
-import reaper
-import MySQLdb
-"""
-def swap(A, B):
-	temp = A
-	A = B
-	B = A
-
-fp = open('ColXCvi.txt')
-fout = open('ColXCvi2.txt', "wb")
-line = fp.readline()
-i = 0
-while line:
-	line2 = map(string.strip, string.split(line.strip()))
-	print len(line2)
-	if i == 0:
-		line2 = line2[:7] + map(lambda X:'ColXCvi' + X, line2[7:])
-	X = line2[1]
-	line2[1] = line2[2]
-	line2[2] = X
-	line2 = line2[:5] + line2[7:]
-	fout.write(string.join(line2[1:], "\t") + "\n")
-	line = fp.readline()
-	i += 1
-	
-fout.close()
-fp.close()
-"""
-"""
-try:
-	#import getpass
-	#passwd = getpass.getpass('Please enter mysql password here : ')
-	con = MySQLdb.Connect(db='db_webqtl',user='webqtlupd',passwd='webqtl', host="opteron")
-	cursor = con.cursor()
-	print "You have successfully connected to mysql.\n"
-except:
-	print "You entered incorrect password.\n"
-	sys.exit(0)
-
-for geno in ("ColXBur.geno", "ColXCvi.geno"):
-	a = reaper.Dataset()
-	a.read(geno)
-	#print a.prgy, len(a.prgy)
-	for item in a.prgy:
-		cursor.execute("insert into Strain(Name, SpeciesId) values(%s, 3)", item)
-		
-cursor.close()
-
-try:
-	#import getpass
-	#passwd = getpass.getpass('Please enter mysql password here : ')
-	con = MySQLdb.Connect(db='db_webqtl',user='webqtlupd',passwd='webqtl', host="opteron")
-	cursor = con.cursor()
-	print "You have successfully connected to mysql.\n"
-except:
-	print "You entered incorrect password.\n"
-	sys.exit(0)
-cursor.execute("select max(Id)+1 from Geno")
-maxId = cursor.fetchone()[0]
-
-for geno in ("ColXBur.geno", "ColXCvi.geno"):
-	a = reaper.Dataset()
-	a.read(geno)
-	#print a.prgy, len(a.prgy)
-	for chr in a:
-		for locus in chr:
-			print geno, locus.name, chr.name, locus.Mb
-			try:
-				cursor.execute("insert into Geno(Id, Name, Chr, MB_UCSC, chr_num, Source, Source2) values(%s, %s, %s, %s, %s, %s, %s)", (maxId, locus.name, chr.name, locus.Mb, chr.name, "Institute for Agronomical Research", "Institute for Agronomical Research"))
-				maxId += 1
-			except:
-				pass
-cursor.close()
-mysql> select max(Id) from Data;
-+----------+
-| max(Id)  |
-+----------+
-| 22163234 |
-+----------+
-1 row in set (0.00 sec)
-
-mysql> select max(DataId) from GenoXRef;
-+-------------+
-| max(DataId) |
-+-------------+
-|    16098047 |
-+-------------+
-1 row in set (0.04 sec)
-
-mysql> select * from Strain order by Id desc limit 5;
-+------+------------+-----------+--------+
-| Id   | Name       | SpeciesId | Symbol |
-+------+------------+-----------+--------+
-| 1828 | ColXCvi499 |         3 | NULL   |
-| 1827 | ColXCvi497 |         3 | NULL   |
-| 1826 | ColXCvi496 |         3 | NULL   |
-| 1825 | ColXCvi495 |         3 | NULL   |
-| 1824 | ColXCvi494 |         3 | NULL   |
-+------+------------+-----------+--------+
-
-"""
-
-"""
-try:
-	#import getpass
-	#passwd = getpass.getpass('Please enter mysql password here : ')
-	con = MySQLdb.Connect(db='db_webqtl',user='webqtlupd',passwd='webqtl', host="opteron")
-	cursor = con.cursor()
-	print "You have successfully connected to mysql.\n"
-except:
-	print "You entered incorrect password.\n"
-	sys.exit(0)
-
-freezeId = 14
-for geno in ("ColXBur.geno", "ColXCvi.geno"):
-	a = reaper.Dataset()
-	a.read(geno)
-	strainIds = []
-	for strain in a.prgy:
-		cursor.execute("select Id from Strain where Name = '%s' and SpeciesId=3" % strain)
-		strainIds.append(cursor.fetchone()[0])
-	for chr in a:
-		for locus in chr:
-			cursor.execute("select max(Id)+1 from Data")
-			dataId = cursor.fetchone()[0]
-			cursor.execute("select Id from Geno where Name = '%s'" % locus.name)
-			GenoId = cursor.fetchone()[0]
-			#print geno, locus.name, chr.name, locus.Mb, dataId, GenoId
-			for i, item in enumerate(locus.genotype):
-				cursor.execute("insert into Data values(%s, %s, %s)" ,(dataId, strainIds[i], item))
-			cursor.execute("insert into GenoXRef values(%s, %s, %s)" , (freezeId, GenoId, dataId))
-	freezeId -= 1
-cursor.close()
-"""
-
-try:
-	#import getpass
-	#passwd = getpass.getpass('Please enter mysql password here : ')
-	con = MySQLdb.Connect(db='db_webqtl',user='webqtlupd',passwd='webqtl', host="opteron")
-	cursor = con.cursor()
-	print "You have successfully connected to mysql.\n"
-except:
-	print "You entered incorrect password.\n"
-	sys.exit(0)
-
-freezeId = 14
-for geno in ("ColXBur.geno", "ColXCvi.geno"):
-	values = [-1, 1, 0, 0]
-	if geno == "ColXBur.geno":
-		strains = ["Col-0", "Bur-0", "ColXBurF1", "BurXColF1"]
-	else:
-		strains = ["Col-0", "Cvi", "ColXCviF1", "CviXColF1"]
-	strainIds = []
-	for strain in strains:
-		cursor.execute("select Id from Strain where Name = '%s' and SpeciesId=3" % strain)
-		strainIds.append(cursor.fetchone()[0])
-	print strainIds
-	cursor.execute("select DataId from GenoXRef where GenoFreezeId = %d" % freezeId)
-	results = cursor.fetchall()
-	for dataId in results:
-		for i, strainId in enumerate(strainIds):
-			#print "insert into Data values(%s, %s, %s)" % (dataId[0], strainId, values[i])
-			cursor.execute("insert into Data values(%s, %s, %s)" ,(dataId[0], strainId, values[i]))
-	freezeId -= 1
-cursor.close()
-