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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20
import string
import time
import re
import math
from math import *
from gn2.base import webqtlConfig
# NL, 07/27/2010. moved from webqtlForm.py
# Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
ParInfo = {
'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'],
'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
'C57BL-6JxC57BL-6NJF2': ['', '', 'C57BL/6J', 'C57BL/6NJ'],
'BXD300': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
'B6BTBRF2': ['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
'BHHBF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
'BHF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
'B6D2F2': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
'BDF2-1999': ['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
'BDF2-2005': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
'CTB6F2': ['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
'CXB': ['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
'AXBXA': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
'AXB': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
'BXA': ['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
'LXS': ['LSF1', 'SLF1', 'ISS', 'ILS'],
'HXBBXH': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
'BayXSha': ['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
'ColXBur': ['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
'ColXCvi': ['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
'SXM': ['SMF1', 'MSF1', 'Steptoe', 'Morex'],
'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
}
#########################################
# Accessory Functions
#########################################
def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits):
from random import choice
_str = prefix[:]
for i in range(length):
_str += choice(chars)
return _str
def ListNotNull(lst):
'''Obsolete - Use built in function any (or all or whatever)
Determine if the elements in a list are all null
'''
for item in lst:
if item is not None:
return 1
return None
def readLineCSV(line): # dcrowell July 2008
"""Parses a CSV string of text and returns a list containing each element as a string.
Used by correlationPage"""
returnList = line.split('","')
returnList[-1] = returnList[-1][:-2]
returnList[0] = returnList[0][1:]
return returnList
def cmpEigenValue(A, B):
try:
if A[0] > B[0]:
return -1
elif A[0] == B[0]:
return 0
else:
return 1
except:
return 0
def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
access_to_confidential_phenotype_trait = 0
if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
access_to_confidential_phenotype_trait = 1
else:
AuthorizedUsersList = [x.strip() for x in authorized_users.split(',')]
if userName in AuthorizedUsersList:
access_to_confidential_phenotype_trait = 1
return access_to_confidential_phenotype_trait
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