From d0911a04958a04042da02a334ccc528dae79cc17 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 27 Mar 2015 20:28:51 +0000
Subject: Removed everything from 'web' directory except genofiles and renamed
 the directory to 'genotype_files'

---
 web/webqtl/intervalAnalyst/GeneUtil.py | 124 ---------------------------------
 1 file changed, 124 deletions(-)
 delete mode 100755 web/webqtl/intervalAnalyst/GeneUtil.py

(limited to 'web/webqtl/intervalAnalyst/GeneUtil.py')

diff --git a/web/webqtl/intervalAnalyst/GeneUtil.py b/web/webqtl/intervalAnalyst/GeneUtil.py
deleted file mode 100755
index 43008ecf..00000000
--- a/web/webqtl/intervalAnalyst/GeneUtil.py
+++ /dev/null
@@ -1,124 +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
-
-#Just return a list of dictionaries
-#each dictionary contains sub-dictionary
-def loadGenes(cursor, chrName, diffCol, startMb, endMb, webqtlDb =None, species='mouse'):
-	#cursor.execute("desc GeneList")
-	#results = cursor.fetchall()
-	#fetchFields = map(lambda X:X[0], results)
-	fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd', 
-	'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID', 
-	'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
-	
-	##List All Species in the Gene Table
-	speciesDict = {}
-	cursor.execute("select Species.Name, GeneList.SpeciesId from Species, GeneList where \
-			GeneList.SpeciesId = Species.Id group by GeneList.SpeciesId")
-	results = cursor.fetchall()
-	for item in results:
-		speciesDict[item[0]] = item[1]
-	
-	##List current Species and other Species
-	speciesId = speciesDict[species]
-	otherSpecies = map(lambda X: [X, speciesDict[X]], speciesDict.keys())
-	otherSpecies.remove([species, speciesId])
-
-	cursor.execute("""SELECT %s from GeneList 
-						where 
-					SpeciesId = %d AND Chromosome = '%s' AND
-					((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f))
-					order by txStart
-					""" 
-					% (string.join(fetchFields, ", "), speciesId, chrName, startMb, endMb, startMb, endMb))
-	results = cursor.fetchall()
-	GeneList = []
-
-	if results:
-		for result in results:
-			newdict = {}
-			for j, item in enumerate(fetchFields):
-				newdict[item] = result[j]
-			#count SNPs if possible	
-			if diffCol and species=='mouse':
-				cursor.execute("""
-					select 
-						count(*) from BXDSnpPosition
-					where 
-						Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
-						StrainId1 = %d AND StrainId2 = %d
-				""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1]))
-				newdict["snpCount"] = cursor.fetchone()[0]
-				newdict["snpDensity"] = newdict["snpCount"]/(newdict["TxEnd"]-newdict["TxStart"])/1000.0
-			else:
-				newdict["snpDensity"] = newdict["snpCount"] = 0
-			
-			try:
-				newdict['GeneLength'] = 1000.0*(newdict['TxEnd'] - newdict['TxStart'])
-			except:
-				pass
-			
-			#load gene from other Species by the same name
-			for item in otherSpecies:
-				othSpec, othSpecId = item
-				newdict2 = {}
-				
-				cursor.execute("SELECT %s from GeneList where SpeciesId = %d and geneSymbol= '%s' limit 1" % 
-							(string.join(fetchFields, ", "), othSpecId, newdict["GeneSymbol"]))
-				resultsOther = cursor.fetchone()
-				if resultsOther:
-					for j, item in enumerate(fetchFields):
-						newdict2[item] = resultsOther[j]
-							
-					#count SNPs if possible, could be a separate function	
-					if diffCol and othSpec == 'mouse':
-						cursor.execute("""
-							select
-								count(*) from BXDSnpPosition
-							where
-								Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND
-								StrainId1 = %d AND StrainId2 = %d
-							""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1]))
-
-						newdict2["snpCount"] = cursor.fetchone()[0]
-						newdict2["snpDensity"] = newdict2["snpCount"]/(newdict2["TxEnd"]-newdict2["TxStart"])/1000.0
-					else:
-						newdict2["snpDensity"] = newdict2["snpCount"] = 0
-						
-					try:
-						newdict2['GeneLength'] = 1000.0*(newdict2['TxEnd'] - newdict2['TxStart'])
-					except:
-						pass
-						
-				newdict['%sGene' % othSpec] = newdict2
-				
-			GeneList.append(newdict)
-
-	return GeneList
-
-
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