###########################################################################
# #
# 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/S_purpuratus/spurpuratus.genedb" % cisRoot
+def buildSpurpuratusDB(db=geneDB):
+ chromoPath = "%s/download/Spur2.1_Nmasked.txt" % cisRoot
+ chromoOutPath = "/S_purpuratus/"
+
+ print "Creating database %s" % db
+ createDBFile(db)
+
+ print "Loading genomic sequence"
+ loadChromosome(db, chromoPath, chromoOutPath)
+
+ print "Creating Indices"
+ createDBindices(db)
+
+ print "Finished creating database %s" % db
+
+def createDBFile(db):
+ spGenome = Genome("spurpuratus", version="2.1", dbFile=db)
+ spGenome.createGeneDB(db)
+
+
def loadChromosome(db, chromPath, chromOutPath):
seqArray = []
seqLen = 0
inFile.close()
-def createDBFile(db):
- spGenome = Genome("spurpuratus", version="2.1", dbFile=db)
- spGenome.createGeneDB(db)
-
-
def createDBindices(db):
spGenome = Genome("spurpuratus", version="2.1", dbFile=db)
spGenome.createIndices()
-
-
-def buildSpurpuratusDB(db=geneDB):
- chromoPath = "%s/download/Spur2.1_Nmasked.txt" % cisRoot
- chromoOutPath = "/S_purpuratus/"
-
- print "Creating database %s" % db
- createDBFile(db)
-
- print "Loading genomic sequence"
- loadChromosome(db, chromoPath, chromoOutPath)
-
- print "Creating Indices"
- createDBindices(db)
-
- print "Finished creating database %s" % db
\ No newline at end of file