first pass cleanup of cistematic/genomes; change bamPreprocessing

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

diff --git a/cistematic/genomes/scerevisiae.py b/cistematic/genomes/scerevisiae.py
index 5866f80963fac6914c81048fb1460548a4ef8a3b..d670c148773fc86b95acbe6d42bf5ae47a1a375f 100644 (file)
--- a/cistematic/genomes/scerevisiae.py
+++ b/cistematic/genomes/scerevisiae.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.                                                 #
@@ -33,33 +33,44 @@ 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_cerevisiae/scerevisiae.genedb" % cisRoot
 
 
-def loadChromosome(db, chromID, chromPath, chromOut):
-    seqArray = []
-    scGenome = Genome("scerevisiae", dbFile=db)
-    inFile = open(chromPath, "r")
-    line = inFile.readline()
-    for line in inFile:
-        seqArray.append(line.strip())
+def buildScerevisiaeDB(db=geneDB):
+    genePath = "%s/download/SGD_features.tab" % cisRoot
+    goDefPath = "%s/download/GO.terms_and_ids" % cisRoot
+    goPath = "%s/download/gene_association.sgd" % cisRoot
 
-    seq = string.join(seqArray, "")
-    seqLen = len(seq)
-    if seqLen < 1:
-        print "Problems reading sequence from file"
+    print "Creating database %s" % db
+    createDBFile(db)
 
-    print "writing to file %s" % chromOut
-    outFile = open("%s%s" % (cisRoot, chromOut), "w")
-    outFile.write(seq)
-    outFile.close()
-    seq = ""
-    print "calling scGenome()"
-    scGenome.addChromosomeEntry(chromID, chromOut, "file")
+    print "Adding gene entries"
+    loadGeneEntries(db, genePath)
+
+    print "Adding gene annotations"
+    loadGeneAnnotations(db, genePath)
+
+    print "Adding gene ontology"
+    loadGeneOntology(db, goPath, goDefPath)
+
+    for chromID in ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16"]:
+        print "Loading chromosome %s" % chromID
+        chromPath = "%s/download/chr%s.fsa" % (cisRoot, chromID)
+        loadChromosome(db, chromID, chromPath, "/S_cerevisiae/chr%s.bin" % chromID)
+
+    print "Creating Indices"
+    createDBindices(db)
+
+    print "Finished creating database %s" % db
+
+
+def createDBFile(db):
+    scGenome = Genome("scerevisiae", version="SGD1",  dbFile=db)
+    scGenome.createGeneDB(db)
 
 
 def loadGeneEntries(db, gFile):
@@ -105,7 +116,7 @@ def loadGeneEntries(db, gFile):
 
 def loadGeneAnnotations(db, annotPath):
     geneAnnotations = []
-    annotFile = open(annotPath, "r")  
+    annotFile = open(annotPath, "r")
     lines = annotFile.readlines()
     annotFile.close()
     scGenome = Genome("scerevisiae", dbFile=db)
@@ -162,55 +173,28 @@ def loadGeneOntology(db, goPath, goDefPath):
     scGenome.addGoInfoBatch(goArray)
 
 
-def createDBFile(db):
-    scGenome = Genome("scerevisiae", version="SGD1",  dbFile=db)
-    scGenome.createGeneDB(db)
+def loadChromosome(db, chromID, chromPath, chromOut):
+    seqArray = []
+    scGenome = Genome("scerevisiae", 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()
+    seq = ""
+    print "calling scGenome()"
+    scGenome.addChromosomeEntry(chromID, chromOut, "file")
 
 
 def createDBindices(db):
     scGenome = Genome("scerevisiae", version="SGD1", dbFile=db)
     scGenome.createIndices()
-
-
-def buildScerevisiaeDB(db=geneDB):
-    genePath = "%s/download/SGD_features.tab" % cisRoot
-    goDefPath = "%s/download/GO.terms_and_ids" % cisRoot
-    goPath = "%s/download/gene_association.sgd" % cisRoot
-    chromos = {"1": "%s/download/chr01.fsa" % cisRoot,
-               "2": "%s/download/chr02.fsa" % cisRoot,
-               "3": "%s/download/chr03.fsa" % cisRoot,
-               "4": "%s/download/chr04.fsa" % cisRoot,
-               "5": "%s/download/chr05.fsa" % cisRoot,
-               "6": "%s/download/chr06.fsa" % cisRoot,
-               "7": "%s/download/chr07.fsa" % cisRoot,
-               "8": "%s/download/chr08.fsa" % cisRoot,
-               "9": "%s/download/chr09.fsa" % cisRoot,
-               "10": "%s/download/chr10.fsa" % cisRoot,
-               "11": "%s/download/chr11.fsa" % cisRoot,
-               "12": "%s/download/chr12.fsa" % cisRoot,
-               "13": "%s/download/chr13.fsa" % cisRoot,
-               "14": "%s/download/chr14.fsa" % cisRoot,
-               "15": "%s/download/chr15.fsa" % cisRoot,
-               "16": "%s/download/chr16.fsa" % cisRoot
-    }
-
-    print "Creating database %s" % db
-    createDBFile(db)
-
-    print "Adding gene entries"
-    loadGeneEntries(db, genePath)
-
-    print "Adding gene annotations"
-    loadGeneAnnotations(db, genePath)
-
-    print "Adding gene ontology"
-    loadGeneOntology(db, goPath, goDefPath)
-
-    for chromID in ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16"]:
-        print "Loading chromosome %s" % chromID
-        loadChromosome(db, chromID, chromos[chromID], "/S_cerevisiae/chr%s.bin" % chromID)
-
-    print "Creating Indices"
-    createDBindices(db)
-
-    print "Finished creating database %s" % db
\ No newline at end of file