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#!/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()
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