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Diffstat (limited to 'gn2/utility/webqtlUtil.py')
-rw-r--r-- | gn2/utility/webqtlUtil.py | 118 |
1 files changed, 118 insertions, 0 deletions
diff --git a/gn2/utility/webqtlUtil.py b/gn2/utility/webqtlUtil.py new file mode 100644 index 00000000..74a6ce4b --- /dev/null +++ b/gn2/utility/webqtlUtil.py @@ -0,0 +1,118 @@ +# 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 |