--- /dev/null
+###########################################################################
+# #
+# C O P Y R I G H T N O T I C E #
+# Copyright (c) 2003-10 by: #
+# * California Institute of Technology #
+# #
+# All Rights Reserved. #
+# #
+# Permission is hereby granted, free of charge, to any person #
+# obtaining a copy of this software and associated documentation files #
+# (the "Software"), to deal in the Software without restriction, #
+# including without limitation the rights to use, copy, modify, merge, #
+# publish, distribute, sublicense, and/or sell copies of the Software, #
+# and to permit persons to whom the Software is furnished to do so, #
+# subject to the following conditions: #
+# #
+# The above copyright notice and this permission notice shall be #
+# included in all copies or substantial portions of the Software. #
+# #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, #
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF #
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND #
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS #
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN #
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN #
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE #
+# SOFTWARE. #
+###########################################################################
+#
+# data for Mus musculus
+import string
+from cistematic.genomes import Genome
+from cistematic.core.geneinfo import geneinfoDB
+from os import environ
+
+if environ.get("CISTEMATIC_ROOT"):
+ cisRoot = environ.get("CISTEMATIC_ROOT")
+else:
+ cisRoot = "/proj/genome"
+
+geneDB = "%s/M_musculus/mmusculus.genedb" % cisRoot
+
+
+def loadChromosome(db, chromID, chromPath, chromOut):
+ seqArray = []
+ mmGenome = Genome("mmusculus", dbFile=db)
+ inFile = open(chromPath, "r")
+ line = inFile.readline()
+ for line in inFile:
+ seqArray.append(line.strip())
+
+ seq = string.join(seqArray, "")
+ seqLen = len(seq)
+ if seqLen < 1:
+ print "Problems reading sequence from file"
+
+ print "writing to file %s" % chromOut
+ outFile = open("%s%s" % (cisRoot, chromOut), "w")
+ outFile.write(seq)
+ outFile.close()
+ mmGenome.addChromosomeEntry(chromID, chromOut, "file")
+
+
+def loadGeneEntries(db, gFile, cDict):
+ """ FIXME - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
+ """
+ geneEntries = []
+ alreadySeen = []
+ mmGenome = Genome("mmusculus", dbFile=db)
+ geneFile = open(gFile, "r")
+ for line in geneFile:
+ cols = line.split("\t")
+ if cols[11].strip() != "GENE" or cols[12] != "C57BL/6J":
+ continue
+
+ chrom = cols[1].strip()
+ if chrom not in cDict:
+ continue
+
+ name = cols[10].split(":")
+ gid = name[1]
+ if gid == "" or gid in alreadySeen:
+ continue
+
+ alreadySeen.append(gid)
+ start = int(cols[2]) - 1
+ stop = int(cols[3]) - 1
+ sense = cols[4]
+ if sense == "+":
+ sense = "F"
+ else:
+ sense = "R"
+
+ geneID = ("mmusculus", gid)
+ gidVersion = 1
+ geneEntries.append((geneID, chrom, start, stop, sense, "gene", gidVersion))
+
+ print "Adding %d gene entries" % len(geneEntries)
+ mmGenome.addGeneEntryBatch(geneEntries)
+
+
+def loadGeneFeatures(db, gFile, cDict):
+ """ Load gene features such as CDS, UTR, and PSEUDO from the gene file.
+ """
+ featureEntries = []
+ mmGenome = Genome("mmusculus", dbFile=db)
+ featureFile = open(gFile, "r")
+ for line in featureFile:
+ cols = line.split("\t")
+ if cols[11].strip() not in ["CDS", "UTR", "PSEUDO"] or cols[12] != "C57BL/6J":
+ continue
+
+ chrom = cols[1].strip()
+ if chrom not in cDict:
+ continue
+
+ fType = cols[11]
+ name = cols[10].split(":")
+ gid = name[1]
+ if gid == "":
+ continue
+
+ start = int(cols[2]) - 1
+ stop = int(cols[3]) - 1
+ sense = cols[4]
+ if sense == "+":
+ sense = "F"
+ else:
+ sense = "R"
+
+ geneID = ("mmusculus", gid)
+ gidVersion = 1
+ featureEntries.append((geneID, gidVersion, chrom, start, stop, sense, fType))
+
+ print "Adding %d feature entries" % len(featureEntries)
+ mmGenome.addFeatureEntryBatch(featureEntries)
+
+
+def loadGeneAnnotations(db):
+ geneAnnotations = []
+ idb = geneinfoDB()
+ mmGenome = Genome("mmusculus", dbFile=db)
+ gidList = mmGenome.allGIDs()
+ for locID in gidList:
+ gID = ("mmusculus", locID)
+ geneDescArray = idb.getDescription(gID)
+ geneDesc = ""
+ for entry in geneDescArray:
+ geneDesc += ","
+ geneDesc += entry.strip()
+
+ if len(geneDescArray) > 0:
+ geneAnnotations.append((gID, string.replace(geneDesc[1:], "'", "p")))
+
+ print "Adding %d annotations" % len(geneAnnotations)
+ mmGenome.addAnnotationBatch(geneAnnotations)
+
+
+def loadGeneOntology(db, goPath, goDefPath):
+ mmGenome = Genome("mmusculus", dbFile=db)
+ goDefFile = open(goDefPath, "r")
+ goFile = open(goPath, "r")
+ idb = geneinfoDB()
+ goDefs = {}
+ goArray = []
+ for goDefEntry in goDefFile:
+ if goDefEntry[0] != "!":
+ cols = goDefEntry.split("\t")
+ goDefs[cols[0]] = (cols[1], cols[2].strip())
+
+ goEntries = goFile.readlines()
+ prevGID = ""
+ for entry in goEntries:
+ try:
+ fields = entry.split("\t")
+ if fields[0] != "10116":
+ continue
+
+ locID = fields[1].strip()
+ gID = ("mmusculus", locID)
+ if prevGID != gID:
+ prevGID = gID
+ gene_name = ""
+ synonyms = idb.geneIDSynonyms(gID)
+ if len(synonyms) >0:
+ for entry in synonyms:
+ gene_name += ","
+ gene_name += entry
+ else:
+ gene_name = " "
+
+ goArray.append((gID, fields[2], "", gene_name[1:], "", string.replace(goDefs[fields[2]][0], "'", "p"), goDefs[fields[2]][1], ""))
+ except:
+ print "locus ID %s could not be added" % locID
+ pass
+
+ print "adding %d go entries" % len(goArray)
+ mmGenome.addGoInfoBatch(goArray)
+
+
+def createDBFile(db):
+ mmGenome = Genome("mmusculus", dbFile=db)
+ mmGenome.createGeneDB(db)
+
+
+def createDBindices(db):
+ mmGenome = Genome("mmusculus", dbFile=db)
+ mmGenome.createIndices()
+
+
+def buildMmusculusDB(db=geneDB, downloadDir="%s/download" % cisRoot):
+ genePath = "%s/seq_gene.md" % downloadDir # ftp://ftp.ncbi.nih.gov/genomes/M_musculus/mapview/seq_gene.md
+ goDefPath = "%s/GO.terms_and_ids" % downloadDir # ftp://ftp.geneontology.org/pub/go/doc/GO.terms_and_ids
+ goPath = "%s/gene2go" % downloadDir # ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz
+ # chromosomes are from ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes
+ # but ignoring all random chromosomes
+ chromDict = {"1": "%s/chr1.fa" % downloadDir,
+ "2": "%s/chr2.fa" % downloadDir,
+ "3": "%s/chr3.fa" % downloadDir,
+ "4": "%s/chr4.fa" % downloadDir,
+ "5": "%s/chr5.fa" % downloadDir,
+ "6": "%s/chr6.fa" % downloadDir,
+ "7": "%s/chr7.fa" % downloadDir,
+ "8": "%s/chr8.fa" % downloadDir,
+ "9": "%s/chr9.fa" % downloadDir,
+ "10": "%s/chr10.fa" % downloadDir,
+ "11": "%s/chr11.fa" % downloadDir,
+ "12": "%s/chr12.fa" % downloadDir,
+ "13": "%s/chr13.fa" % downloadDir,
+ "14": "%s/chr14.fa" % downloadDir,
+ "15": "%s/chr15.fa" % downloadDir,
+ "16": "%s/chr16.fa" % downloadDir,
+ "17": "%s/chr17.fa" % downloadDir,
+ "18": "%s/chr18.fa" % downloadDir,
+ "19": "%s/chr19.fa" % downloadDir,
+ "X": "%s/chrX.fa" % downloadDir,
+ "Y": "%s/chrY.fa" % downloadDir,
+ "M": "%s/chrM.fa" % downloadDir
+ }
+
+ print "Creating database %s" % db
+ createDBFile(db)
+
+ print "Adding gene entries"
+ loadGeneEntries(db, genePath, chromDict)
+
+ print "Adding gene features"
+ loadGeneFeatures(db, genePath, chromDict)
+
+ print "Adding gene annotations"
+ loadGeneAnnotations(db)
+
+ print "Adding gene ontology"
+ loadGeneOntology(db, goPath, goDefPath)
+
+ for chromID in chromDict.keys():
+ print "Loading chromosome %s" % chromID
+ loadChromosome(db, chromID, chromDict[chromID], "/M_musculus/chromo%s.bin" % chromID)
+
+ print "Creating Indices"
+ createDBindices(db)
+
+ print "Finished creating database %s" % db
\ No newline at end of file