Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

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