###########################################################################
# #
# 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"
-geneDB = "%s/B_taurus/btaurus.genedb" % cisRoot
+geneDB = "%s/B_taurus/btaurus.genedb" % cisRoot
-def loadChromosome(db, chromPath, chromOutPath):
- seqArray = []
- seqLen = 0
- btGenome = Genome("btaurus", dbFile=db)
- inFile = open(chromPath, "r")
- header = inFile.readline()
- while header != "":
- seqArray = []
- seqLen = 0
- chromID = header.strip()[1:]
- currentLine = inFile.readline()
+def buildBtaurusDB(db=geneDB):
+ genePath = "%s/download/bt2/genscan.txt" % cisRoot
+ chromoPath = "%s/download/bt2/bosTau2.softmask2.fa" % cisRoot
+ chromoOutPath = "/B_taurus/"
- while currentLine != "" and currentLine[0] != ">":
- lineSeq = currentLine.strip()
- seqLen += len(lineSeq)
- seqArray.append(lineSeq)
- currentLine = inFile.readline()
+ print "Creating database %s" % db
+ createDBFile(db)
- seq = string.join(seqArray, "")
- if seqLen < 500000:
- print "Added contig %s to database" % chromID
- btGenome.addSequence(("btaurus", chromID), seq, "chromosome", str(seqLen))
- btGenome.addChromosomeEntry(chromID, chromID, "db")
- else:
- outFileName = "%s%s.bin" % (chromOutPath, chromID)
- outFile = open("%s%s" % (cisRoot, outFileName), "w")
- outFile.write(seq)
- outFile.close()
- print "Added contig file %s to database" % outFileName
- btGenome.addChromosomeEntry(chromID, outFileName, "file")
+ print "Adding gene entries"
+ loadGeneEntries(db, genePath)
- header = currentLine
+ print "Adding gene features"
+ loadGeneFeatures(db, genePath)
- inFile.close()
+ print "Loading sequences"
+ loadChromosome(db, chromoPath, chromoOutPath)
+
+ print "Creating Indices"
+ createDBindices(db)
+
+ print "Finished creating database %s" % db
+
+
+def createDBFile(db):
+ btGenome = Genome("btaurus", dbFile=db)
+ btGenome.createGeneDB(db)
def loadGeneEntries(db, gFile):
- """ FIXME - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
- """
+ #TODO: - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
+
geneEntries = []
btGenome = Genome("btaurus", dbFile=db)
geneFile = open(gFile, "r")
btGenome.addGeneEntryBatch(geneEntries)
-def loadGeneAnnotations(db, annotPath):
- geneAnnotations = []
- annotFile = open(annotPath, "r")
- btGenome = Genome("btaurus", dbFile=db)
- for line in annotFile:
- try:
- cols = line.split("\t")
- locID = cols[0]
- geneDesc = cols[6]
- if len(locID) > 0:
- geneAnnotations.append((("btaurus", locID), string.replace(geneDesc.strip(), "'", "p")))
- except:
- pass
-
- print "Adding %d annotations" % len(geneAnnotations)
- btGenome.addAnnotationBatch(geneAnnotations)
-
-
def loadGeneFeatures(db, gfile):
geneFile = open(gfile, "r")
senseArray = {"+": "F",
btGenome.addFeatureEntryBatch(insertArray)
+def loadGeneAnnotations(db, annotPath):
+ geneAnnotations = []
+ annotFile = open(annotPath, "r")
+ btGenome = Genome("btaurus", dbFile=db)
+ for line in annotFile:
+ try:
+ cols = line.split("\t")
+ locID = cols[0]
+ geneDesc = cols[6]
+ if len(locID) > 0:
+ geneAnnotations.append((("btaurus", locID), string.replace(geneDesc.strip(), "'", "p")))
+ except:
+ pass
+
+ print "Adding %d annotations" % len(geneAnnotations)
+ btGenome.addAnnotationBatch(geneAnnotations)
+
+
def loadGeneOntology(db, goPath, goDefPath, annotPath):
btGenome = Genome("btaurus", 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()
btGenome.addGoInfoBatch(goArray)
-def createDBFile(db):
- btGenome = Genome("btaurus", dbFile=db)
- btGenome.createGeneDB(db)
-
-
-def createDBindices(db):
+def loadChromosome(db, chromPath, chromOutPath):
+ seqArray = []
+ seqLen = 0
btGenome = Genome("btaurus", dbFile=db)
- btGenome.createIndices()
-
+ inFile = open(chromPath, "r")
+ header = inFile.readline()
+ while header != "":
+ seqArray = []
+ seqLen = 0
+ chromID = header.strip()[1:]
+ currentLine = inFile.readline()
-def buildBtaurusDB(db=geneDB):
- genePath = "%s/download/bt2/genscan.txt" % cisRoot
- chromoPath = "%s/download/bt2/bosTau2.softmask2.fa" % cisRoot
- chromoOutPath = "/B_taurus/"
-
- print "Creating database %s" % db
- createDBFile(db)
+ while currentLine != "" and currentLine[0] != ">":
+ lineSeq = currentLine.strip()
+ seqLen += len(lineSeq)
+ seqArray.append(lineSeq)
+ currentLine = inFile.readline()
- print "Adding gene entries"
- loadGeneEntries(db, genePath)
+ seq = string.join(seqArray, "")
+ if seqLen < 500000:
+ print "Added contig %s to database" % chromID
+ btGenome.addSequence(("btaurus", chromID), seq, "chromosome", str(seqLen))
+ btGenome.addChromosomeEntry(chromID, chromID, "db")
+ else:
+ outFileName = "%s%s.bin" % (chromOutPath, chromID)
+ outFile = open("%s%s" % (cisRoot, outFileName), "w")
+ outFile.write(seq)
+ outFile.close()
+ print "Added contig file %s to database" % outFileName
+ btGenome.addChromosomeEntry(chromID, outFileName, "file")
- print "Adding gene features"
- loadGeneFeatures(db, genePath)
+ header = currentLine
- print "Loading sequences"
- loadChromosome(db, chromoPath, chromoOutPath)
+ inFile.close()
- print "Creating Indices"
- createDBindices(db)
- print "Finished creating database %s" % db
\ No newline at end of file
+def createDBindices(db):
+ btGenome = Genome("btaurus", dbFile=db)
+ btGenome.createIndices()
projects / erange.git / blobdiff