Adding genotypes and new_genotypes (json files) directories to git

so they can be pulled to the new EC2 server

1 files changed, 170 insertions, 0 deletions

diff --git a/web/genotypes/process.py b/web/genotypes/process.py
new file mode 100755
index 00000000..96cbc9b4
--- /dev/null
+++ b/web/genotypes/process.py
@@ -0,0 +1,170 @@
+#!/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()
+