path: root/scripts/maintenance/readProbeSetSE_v7.py

#!/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
# This version fix the bug that incorrectly exclude the first 2 probesetIDs
########################################################################

import string
import sys
import MySQLdb
import getpass
import time


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

#GeneChipId = 4
#dataStart = 1
# ProbeSetFreezeId = 359 #JAX Liver 6C Affy M430 2.0 (Jul11) MDP
#fp = open("GSE10493_AllSamples_6C_Z_AvgSE.txt", 'rb')


#########################################################################
#
#  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 = header.strip().split('\t')
header = [item.strip() for item in header]
nfield = len(header)
line = fp.readline()

kj = 0
while line:
    line2 = line.strip().split('\t')
    line2 = [item.strip() for item in line2]
    if len(line2) != nfield:
        isCont = 0
        print(("Error : " + line))

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

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

GeneList = sorted(map(string.lower, GeneList))

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 = header.strip().split('\t')
header = [item.strip() for item in header]
header = list(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:
        isCont = 0
        print((item, 'does not exist, check the if the strain name is correct'))

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 = line.strip().split('\t')
line2 = [x.strip() for x in 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])
    Names = sorted(map(string.lower, Names))

##---- 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")
    isCont = 0

    print((item, " doesn't exist"))
if isCont == 0:
    sys.exit(0)


print(('used ', time.time()-time0, ' seconds'))
#############################
# Insert new Data into SE
############################
db.execute("""
        select ProbeSet.%s, ProbeSetXRef.DataId from ProbeSet, ProbeSetXRef
        where ProbeSet.Id=ProbeSetXRef.ProbeSetId and ProbeSetXRef.ProbeSetFreezeId=%d"""
           % (IdStr, ProbeSetFreezeId))
results = db.fetchall()

ProbeNameId = {}
for Name, Id in results:
    ProbeNameId[Name] = Id

ferror = open("ProbeError.txt", "wb")

DataValues = []

fp.seek(0)  # XZ add this line
line = fp.readline()  # XZ add this line
line = fp.readline()

kj = 0
while line:
    line2 = line.strip().split('\t')
    line2 = [x.strip() for x in line2]

    CellId = line2[0]
    if CellId not in ProbeNameId:
        ferror.write(CellId + " doesn't exist\n")
    else:
        DataId = ProbeNameId[CellId]
        datasorig = line2[dataStart:]

        i = 0
        for item in datasorig:
            if item != '':
                value = '('+str(DataId)+','+str(Ids[i])+','+str(item)+')'
                DataValues.append(value)
                i += 1

    kj += 1
    if kj % 100 == 0:
        Dataitems = ','.join(DataValues)
        cmd = 'insert ProbeSetSE values %s' % Dataitems
        db.execute(cmd)

        DataValues = []
        line = fp.readline()
        print((CellId, " doesn't exist"))
        print(('inserted ', kj, ' lines'))
        print(('used ', time.time()-time0, ' seconds'))

if len(DataValues) > 0:
    DataValues = ','.join(DataValues)
    cmd = 'insert ProbeSetSE values %s' % DataValues
    db.execute(cmd)

db.close()
con.close()