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Diffstat (limited to 'web/webqtl/textUI/cmdMap.py')
| -rwxr-xr-x | web/webqtl/textUI/cmdMap.py | 144 |
1 files changed, 144 insertions, 0 deletions
diff --git a/web/webqtl/textUI/cmdMap.py b/web/webqtl/textUI/cmdMap.py new file mode 100755 index 00000000..1fbff5a5 --- /dev/null +++ b/web/webqtl/textUI/cmdMap.py @@ -0,0 +1,144 @@ +# 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 |