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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 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
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