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authorroot2012-05-08 18:39:56 -0500
committerroot2012-05-08 18:39:56 -0500
commitea46f42ee640928b92947bfb204c41a482d80937 (patch)
tree9b27a4eb852d12539b543c3efee9d2a47ef470f3 /web/webqtl/intervalAnalyst/GeneUtil.py
parent056b5253fc3857b0444382aa39944f6344dc1ceb (diff)
downloadgenenetwork2-ea46f42ee640928b92947bfb204c41a482d80937.tar.gz
Add all the source codes into the github.
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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
+
+