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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
#########################################
# Interval Mapping Class
#########################################
class cmdInterval(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=pos&return=100&chr=12">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&sort=pos&return=100&chr=12</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
if self.accessError:
return
self.sort = None
self.step = 0.01
self.peak = 1
self.chr = None
self.sort = None
self.returnnumber = 20
if self.error:
self.error = 1
self.contents.append(self.example)
return
else:
try:
self.sort = self.data.getvalue('sort')
if string.lower(self.sort) == 'pos':
self.sort = 'pos'
else:
self.sort = 'lrs'
except:
self.sort = None
try:
self.returnnumber = int(self.data.getvalue('return'))
except:
self.returnnumber = 20
try:
self.chr = self.data.getvalue('chr')
except:
self.chr = None
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
dataset0 = reaper.Dataset()
dataset0.read(os.path.join(webqtlConfig.GENODIR, RISet + '.geno'))
strainList = list(dataset0.prgy)
dataset = dataset0.addinterval()
if self.chr != None:
for _chr in dataset:
if string.lower(_chr.name) == string.lower(self.chr):
dataset.chromosome = [_chr]
break
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)
#print inter1[0]
returnPeak = []
nqtl = len(qtlscan)
if self.peak:
for i in range(nqtl):
if i == 0 or qtlscan[i].locus.chr != qtlscan[i-1].locus.chr:
if qtlscan[i].lrs < qtlscan[i+1].lrs:
continue
elif i == nqtl-1 or qtlscan[i].locus.chr != qtlscan[i+1].locus.chr:
if qtlscan[i].lrs < qtlscan[i-1].lrs:
continue
else:
if qtlscan[i].lrs < qtlscan[i+1].lrs or qtlscan[i].lrs < qtlscan[i-1].lrs:
continue
returnPeak.append(qtlscan[i])
else:
returnPeak = qtlscan[:]
if returnPeak:
self.contents.append("Locus\tLRS\tChr\tAdditive\tp-value\tcM")
qtlresult = []
for item in returnPeak:
p_value = reaper.pvalue(item.lrs,LRS)
qtlresult.append((item.locus.name,item.lrs,item.locus.chr,item.additive,p_value, item.locus.cM))
if self.sort == 'lrs':
qtlresult.sort(self.cmpLRS2)
for item in qtlresult:
self.contents.append("%s\t%2.4f\t%s\t%2.4f\t%1.4f\t%s" % item)
else:
self.contents.append("###Error: Error occurs while regression.")
return
def cmpPValue(self,A,B):
try:
if A[-1] > B[-1]:
return 1
elif A[-1] == B[-1]:
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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