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Diffstat (limited to 'web/webqtl/textUI/cmdMap.py')
| -rwxr-xr-x | web/webqtl/textUI/cmdMap.py | 144 |
1 files changed, 0 insertions, 144 deletions
diff --git a/web/webqtl/textUI/cmdMap.py b/web/webqtl/textUI/cmdMap.py deleted file mode 100755 index 1fbff5a5..00000000 --- a/web/webqtl/textUI/cmdMap.py +++ /dev/null @@ -1,144 +0,0 @@ -# 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 os - -import reaper - -from base import webqtlConfig -from cmdClass import cmdClass - - -######################################### -# Mapping Class -######################################### -class cmdMap(cmdClass): - - def __init__(self,fd=None): - - cmdClass.__init__(self,fd) - - if not webqtlConfig.TEXTUI: - self.contents.append("Please send your request to http://robot.genenetwork.org") - return - - self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=lrs&return=20</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID) - if self.accessError: - return - try: - self.returnnumber = int(self.data.getvalue('return')) - except: - self.returnnumber = None - - if self.error: - self.contents.append(self.example) - self.contents.append(self.accessCode) - else: - self.sort = self.data.getvalue('sort') - self.readDB() - - def readDB(self): - prefix, dbId = self.getDBId(self.database) - if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")): - self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - RISet = self.getRISet(prefix, dbId) - traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe) - if not traitdata: - self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.") - self.contents.append(self.example) - self.contents.append(self.accessCode) - return - - dataset = reaper.Dataset() - dataset.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno')) - strainList = list(dataset.prgy) - - strains = [] - trait = [] - _prgy = dataset.prgy - for item in traitdata: - if item[0] in _prgy: - strains.append(item[0]) - trait.append(item[1]) - - qtlscan = dataset.regression(strains, trait) - LRS = dataset.permutation(strains, trait) - nperm = len(LRS) - if qtlscan: - self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value") - qtlresult = [] - if self.returnnumber: - self.returnnumber = min(self.returnnumber,len(qtlscan)) - if self.sort == 'lrs': - qtlscan.sort(self.cmpLRS) - for item in qtlscan[:self.returnnumber]: - p_value = reaper.pvalue(item.lrs,LRS) - qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value)) - else:#sort by position - qtlscan2 = qtlscan[:] - qtlscan2.sort(self.cmpLRS) - LRSthresh = qtlscan2[self.returnnumber].lrs - for item in qtlscan: - if item.lrs >= LRSthresh: - p_value = reaper.pvalue(item.lrs,LRS) - qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value)) - else: - for item in qtlscan: - p_value = reaper.pvalue(item.lrs,LRS) - qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value)) - if self.sort == 'lrs': - qtlresult.sort(self.cmpLRS2) - for item in qtlresult: - self.contents.append("%s\t%2.5f\t%s\t%2.5f\t%1.5f" % item) - else: - self.contents.append("###Error: Error occurs while regression.") - return - - def cmpLRS(self,A,B): - try: - if A.lrs < B.lrs: - return 1 - elif A.lrs == B.lrs: - return 0 - else: - return -1 - except: - return 0 - - def cmpLRS2(self,A,B): - try: - if A[1] < B[1]: - return 1 - elif A[1] == B[1]: - return 0 - else: - return -1 - except: - return 0 |