###########################################################################
# #
# C O P Y R I G H T N O T I C E #
-# Copyright (c) 2003-10 by: #
+# Copyright (c) 2003-13 by: #
# * California Institute of Technology #
# #
# All Rights Reserved. #
from os import environ
if environ.get("CISTEMATIC_ROOT"):
- cisRoot = environ.get("CISTEMATIC_ROOT")
+ cisRoot = environ.get("CISTEMATIC_ROOT")
else:
cisRoot = "/proj/genome"
"Z": "26"
}
-def loadChromosome(db, chromID, chromPath, chromOut):
- seqArray = []
- dmGenome = Genome("dmelanogaster", 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"
+def buildDmelanogasterDB(db=geneDB):
+ """ genes and annotations are from UCSC. GO association file is from geneontology.org.
+ """
+ genePath = "%s/download/flyBaseGene.txt" % cisRoot
+ annotPath = "%s/download/gene_info" % cisRoot
+ goDefPath = "%s/download/GO.terms_and_ids" % cisRoot
+ goPath = "%s/download/gene2go" % cisRoot
- print "writing to file %s" % chromOut
- outFile = open("%s%s" % (cisRoot, chromOut), "w")
- outFile.write(seq)
- outFile.close()
- dmGenome.addChromosomeEntry(chromID, chromOut, "file")
+ print "Creating database %s" % db
+ createDBFile(db)
+
+ print "Adding gene entries"
+ loadGeneEntries(db, genePath)
+
+ print "Adding gene features"
+ loadGeneFeatures(db, genePath)
+
+ print "Adding gene annotations"
+ loadGeneAnnotations(db, annotPath)
+
+ print "Adding gene ontology"
+ loadGeneOntology(db, goPath, goDefPath, annotPath)
+
+ chromList = ["2L", "2R", "2LHet", "2RHet", "3L", "3R", "3LHet", "3RHet",
+ "4", "X", "XHet", "YHet", "U", "UExtra", "M"
+ ]
+ for chromID in chromList:
+ print "Loading chromosome %s" % chromID
+ chromPath = "%s/download/chr%s.fa" % (cisRoot, chromID)
+ loadChromosome(db, chromID, chromPath, "/D_melanogaster/chromo%s.bin" % chromID)
+
+ print "Creating Indices"
+ createDBindices(db)
+
+ print "Finished creating database %s" % db
+
+
+def createDBFile(db):
+ dmGenome = Genome("dmelanogaster", dbFile=db)
+ dmGenome.createGeneDB(db)
def loadGeneEntries(db, gFile):
def loadGeneAnnotations(db, annotPath):
geneAnnotations = []
- annotFile = open(annotPath, "r")
+ annotFile = open(annotPath, "r")
dmGenome = Genome("dmelanogaster", dbFile=db)
for line in annotFile:
try:
dmGenome = Genome("dmelanogaster", dbFile=db)
goDefFile = open(goDefPath, "r")
goFile = open(goPath, "r")
- annotFile = open(annotPath, "r")
+ annotFile = open(annotPath, "r")
annotEntries = annotFile.readlines()
annotFile.close()
goDefEntries = goDefFile.readlines()
dmGenome.addGoInfoBatch(goArray)
-def createDBFile(db):
+def loadChromosome(db, chromID, chromPath, chromOut):
+ seqArray = []
dmGenome = Genome("dmelanogaster", dbFile=db)
- dmGenome.createGeneDB(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()
+ dmGenome.addChromosomeEntry(chromID, chromOut, "file")
def createDBindices(db):
dmGenome = Genome("dmelanogaster", dbFile=db)
dmGenome.createIndices()
-
-
-def buildDmelanogasterDB(db=geneDB):
- """ genes and annotations are from UCSC. GO association file is from geneontology.org.
- """
- genePath = "%s/download/flyBaseGene.txt" % cisRoot
- annotPath = "%s/download/gene_info" % cisRoot
- goDefPath = "%s/download/GO.terms_and_ids" % cisRoot
- goPath = "%s/download/gene2go" % cisRoot
- chromos = {"2L": "%s/download/chr2L.fa" % cisRoot,
- "2R": "%s/download/chr2R.fa" % cisRoot,
- "2LHet": "%s/download/chr2LHet.fa" % cisRoot,
- "2RHet": "%s/download/chr2RHet.fa" % cisRoot,
- "3L": "%s/download/chr3L.fa" % cisRoot,
- "3LHet": "%s/download/chr3LHet.fa" % cisRoot,
- "3R": "%s/download/chr3R.fa" % cisRoot,
- "3RHet": "%s/download/chr3RHet.fa" % cisRoot,
- "4": "%s/download/chr4.fa" % cisRoot,
- "X": "%s/download/chrX.fa" % cisRoot,
- "XHet": "%s/download/chrXHet.fa" % cisRoot,
- "YHet": "%s/download/chrYHet.fa" % cisRoot,
- "U": "%s/download/chrU.fa" % cisRoot,
- "Uextra": "%s/download/chrUextra.fa" % cisRoot,
- "M": "%s/download/chrM.fa" % cisRoot
- }
-
- print "Creating database %s" % db
- createDBFile(db)
-
- print "Adding gene entries"
- loadGeneEntries(db, genePath)
-
- print "Adding gene features"
- loadGeneFeatures(db, genePath)
-
- print "Adding gene annotations"
- loadGeneAnnotations(db, annotPath)
-
- print "Adding gene ontology"
- loadGeneOntology(db, goPath, goDefPath, annotPath)
-
- for chromID in chromos.keys():
- print "Loading chromosome %s" % chromID
- loadChromosome(db, chromID, chromos[chromID], "/D_melanogaster/chromo%s.bin" % chromID)
-
- print "Creating Indices"
- createDBindices(db)
-
- print "Finished creating database %s" % db
\ No newline at end of file