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authorzsloan2015-03-27 20:28:51 +0000
committerzsloan2015-03-27 20:28:51 +0000
commitd0911a04958a04042da02a334ccc528dae79cc17 (patch)
tree3c48e2e937c1dbeaf00a5697c87ed251afa5c8f1 /web/webqtl/textUI/cmdInterval.py
parenta840ad18e1fe3db98a359a159e9b9b72367a2839 (diff)
downloadgenenetwork2-d0911a04958a04042da02a334ccc528dae79cc17.tar.gz
Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'
Diffstat (limited to 'web/webqtl/textUI/cmdInterval.py')
-rwxr-xr-xweb/webqtl/textUI/cmdInterval.py174
1 files changed, 0 insertions, 174 deletions
diff --git a/web/webqtl/textUI/cmdInterval.py b/web/webqtl/textUI/cmdInterval.py
deleted file mode 100755
index 0b97c7c3..00000000
--- a/web/webqtl/textUI/cmdInterval.py
+++ /dev/null
@@ -1,174 +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
-
-#########################################
-# 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
-
-