first pass cleanup of cistematic/genomes; change bamPreprocessing

[erange.git] / cistematic / genomes / spurpuratus.py

diff --git a/cistematic/genomes/spurpuratus.py b/cistematic/genomes/spurpuratus.py
index 6098562b45b54ea2916987552587e95ab50ab8df..e9d12b77a02f880d55082afe10e31132e6e187fd 100644 (file)
--- a/cistematic/genomes/spurpuratus.py
+++ b/cistematic/genomes/spurpuratus.py
@@ -1,7 +1,7 @@
 ###########################################################################
 #                                                                         #
 # 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.                                                 #
@@ -33,13 +33,33 @@ from cistematic.genomes import Genome
 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
@@ -82,27 +102,6 @@ def loadChromosome(db, chromPath, chromOutPath):
     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