#!/usr/bin/python2
"""This script use the nearest marker to the transcript as control, increasing permutation rounds according to the p-value"""

########################################################################
# Last Updated Sep 27, 2011 by Xiaodong
########################################################################
import string
import sys
import MySQLdb
import getpass
import time
#import pdb

#pdb.set_trace()

########################################################################

def translateAlias(str):
	if str == "B6":
		return "C57BL/6J"
	elif str == "D2":
		return "DBA/2J"
	else:
		return str

########################################################################
#
#  Indicate Data Start Position, ProbeFreezeId, GeneChipId, DataFile
#
########################################################################

dataStart = 1

GeneChipId = int( input("Enter GeneChipId:") )
ProbeSetFreezeId = int( input("Enter ProbeSetFreezeId:") )
input_file_name = input("Enter file name with suffix:")

fp = open("%s" % input_file_name, 'rb')

try:
        passwd = getpass.getpass('Please enter mysql password here : ') 
        con = MySQLdb.Connect(db='db_webqtl',host='localhost', user='username',passwd=passwd)

        db = con.cursor()
        print("You have successfully connected to mysql.\n")
except:
        print("You entered incorrect password.\n")
        sys.exit(0)

time0 = time.time()

#########################################################################
#
#  Check if each line have same number of members
#  generate the gene list of expression data here
#
#########################################################################
print('Checking if each line have same number of members')

GeneList = []
isCont = 1
header = fp.readline()
header = string.split(string.strip(header),'\t')
header = map(string.strip, header)
nfield = len(header)
line = fp.readline()

kj=0
while line:
	line2 = string.split(string.strip(line),'\t')
	line2 = map(string.strip, line2)
	if len(line2) != nfield:
		print(("Error : " + line))
		isCont = 0

	GeneList.append(line2[0])
	line = fp.readline()

	kj+=1
	if kj%100000 == 0:
		print(('checked ',kj,' lines'))

GeneList = map(string.lower, GeneList)
GeneList.sort()
	
if isCont==0:
	sys.exit(0)


print(('used ',time.time()-time0,' seconds'))
#########################################################################
#
#  Check if each strain exist in database
#  generate the string id list of expression data here
#
#########################################################################
print('Checking if each strain exist in database')

isCont = 1
fp.seek(0)
header = fp.readline()
header = string.split(string.strip(header),'\t')
header = map(string.strip, header)
header = map(translateAlias, header)
header = header[dataStart:]
Ids = []
for item in header:
	try:
		db.execute('select Id from Strain where Name = "%s"' % item)
		Ids.append(db.fetchall()[0][0])
	except:
		print((item,'does not exist, check the if the strain name is correct'))
		isCont=0

if isCont==0:
	sys.exit(0)


print(('used ',time.time()-time0,' seconds'))
########################################################################
#
# Check if each ProbeSet exist in database
#
########################################################################
print('Check if each ProbeSet exist in database')

##---- find PID is name or target ----##
line = fp.readline()
line = fp.readline()
line2 = string.split(string.strip(line),'\t')
line2 = map(string.strip, line2)
PId = line2[0]

db.execute('select Id from ProbeSet where Name="%s" and ChipId=%d' % (PId, GeneChipId) )
results = db.fetchall()
IdStr = 'TargetId'
if len(results)>0:
	IdStr = 'Name'


##---- get Name/TargetId list from database ----##
db.execute('select distinct(%s) from ProbeSet where ChipId=%d order by %s' % (IdStr, GeneChipId, IdStr))
results = db.fetchall()
	
Names = []
for item in results:
	Names.append(item[0])
	
print(Names)

Names = map(string.lower, Names)

Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at  doesn't exist --#


##---- compare genelist with names ----##
x=y=0
x1=-1
GeneList2=[]
while x<len(GeneList) and y<len(Names):
	if GeneList[x]==Names[y]:
		x += 1
		y += 1
	elif GeneList[x]<Names[y]:
		if x!=x1:
			GeneList2.append(GeneList[x])
			x1 = x
		x += 1
	elif GeneList[x]>Names[y]:
		y += 1

	if x%100000==0:
		print(('check Name, checked %d lines'%x))

while x<len(GeneList):
	GeneList2.append(GeneList[x])
	x += 1

isCont=1
ferror = open("ProbeSetError.txt", "wb")
for item in GeneList2:
	ferror.write(item + " doesn't exist \n")
	print((item, " doesn't exist, check if the ProbeSet name is correct"))
	isCont = 0
        
if isCont==0:
	sys.exit(0)


print(('used ',time.time()-time0,' seconds'))
#########################################################################
#
# Insert data into database
#
#########################################################################
print('getting ProbeSet/Id')


#---- get Name/Id map ----#
db.execute('select %s, Id from ProbeSet where ChipId=%d order by %s' % (IdStr, GeneChipId, IdStr))
results = db.fetchall()
NameIds = {}
for item in results:
	NameIds[item[0]] = item[1]
print(('used ',time.time()-time0,' seconds'))


print('inserting data')

##---- get old max dataId ----##
db.execute('select max(Id) from ProbeSetData')
maxDataId = int(db.fetchall()[0][0])
bmax = maxDataId
print(("old_max = %d\n" % bmax))

##---- insert data ----##
fp.seek(0)
line = fp.readline()
line = fp.readline()
kj = 0

values1 = []
values2 = []
while line:
	line2 = string.split(string.strip(line),'\t')
	line2 = map(string.strip, line2)
	PId = line2[0]
	recordId = NameIds[PId]

	maxDataId += 1
	datasorig = line2[dataStart:]
	
	###### Data Table items ######
	i=0
	for item in datasorig:
		try:
			values1.append('(%d,%d,%s)' % (maxDataId, Ids[i], float(item)))
      		except:
			pass
		i += 1

	values2.append("(%d,%d,%d)" % (ProbeSetFreezeId, recordId, maxDataId))


	##---- insert into table ----##
	kj += 1
	if kj % 100 == 0:
		cmd = ','.join(values1)
		cmd = 'insert into ProbeSetData values %s' % cmd
		db.execute(cmd)

		cmd = ','.join(values2)
		cmd = 'insert into ProbeSetXRef(ProbeSetFreezeId, ProbeSetId, DataId) values %s' % cmd
		db.execute(cmd)

		values1=[]
		values2=[]
		print(('Inserted ', kj,' lines'))
		print(('used ',time.time()-time0,' seconds'))
	
	line = fp.readline()



if len(values1)>0:
	cmd = ','.join(values1)
	cmd = 'insert into ProbeSetData values %s' % cmd
	db.execute(cmd)

	cmd = ','.join(values2)
	cmd = 'insert into ProbeSetXRef(ProbeSetFreezeId, ProbeSetId, DataId) values %s' % cmd
	db.execute(cmd)

con.close()