<commit_before>#!/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(raw_input("Enter GeneChipId:"))
ProbeSetFreezeId = int(raw_input("Enter ProbeSetFreezeId:"))
input_file_name = raw_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=<PASSWORD>)

    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<commit_msg>Convert `raw_input` to `input`<commit_after>#!/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 = <PASSWORD>pass('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
{'fraction_non_alphanumeric': 0.3376590330788804, 'fraction_numerical': 0.0183206106870229, 'mean_word_length': 5.412724306688418, 'pattern_counts': {'":': 4, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4613453', 'n_tokens_mistral': 1119, 'n_tokens_neox': 998, 'n_words': 300}