Add all the source codes into the github.

1 files changed, 124 insertions, 0 deletions

diff --git a/web/webqtl/intervalAnalyst/GeneUtil.py b/web/webqtl/intervalAnalyst/GeneUtil.py
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+++ b/web/webqtl/intervalAnalyst/GeneUtil.py
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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
+
+#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
+
+