###########################################################################
# #
# 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/C_familiaris/cfamiliaris.genedb" % cisRoot
-def loadChromosome(db, chromID, chromPath, chromOut):
- seqArray = []
- cfGenome = Genome("cfamiliaris", dbFile=db)
- inFile = open(chromPath, "r")
- line = inFile.readline()
- for line in inFile:
- seqArray.append(line.strip())
+def buildDogDB(db=geneDB):
+ genePath = "%s/download/seq_gene.md" % cisRoot
+ print "Creating database %s" % db
+ createDBFile(db)
- seq = string.join(seqArray, "")
- seqLen = len(seq)
- if seqLen < 1:
- print "Problems reading sequence from file"
+ print "Adding gene entries"
+ loadGeneEntries(db, genePath)
- print "writing to file %s" % chromOut
- outFile = open("%s%s" % (cisRoot, chromOut), "w")
- outFile.write(seq)
- outFile.close()
- cfGenome.addChromosomeEntry(chromID, chromOut, "file")
+ print "Adding gene features"
+ loadGeneFeatures(db, genePath)
+
+ chromList = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10",
+ "11", "12", "13", "14", "15", "16", "17", "18", "19", "20",
+ "21", "22", "23", "24", "25", "26", "27", "28", "29", "30",
+ "31", "32", "33", "34", "35", "36", "37", "38", "X", "Un"
+ ]
+ for chromID in chromList:
+ print "Loading chromosome %s" % chromID
+ chromPath = "%s/download/chr%s.fa" % (cisRoot, chromID)
+ loadChromosome(db, chromID, chromPath, "/C_familiaris/chromo%s.bin" % chromID)
+
+ print "Creating Indices"
+ createDBindices(db)
+
+ print "Finished creating database %s" % db
+
+
+def createDBFile(db):
+ cfGenome = Genome("cfamiliaris", dbFile=db)
+ cfGenome.createGeneDB(db)
def loadGeneEntries(db, gFile):
- """ FIXME - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
- """
+ #TODO: - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
+
geneEntries = []
alreadySeen = []
cfGenome = Genome("cfamiliaris", dbFile=db)
synonyms = idb.geneIDSynonyms(gID)
if len(synonyms) >0:
for entry in synonyms:
- gene_name += ","
+ gene_name += ","
gene_name += entry
else:
gene_name = " "
cfGenome.addGoInfoBatch(goArray)
-def createDBFile(db):
- cfGenome = Genome("cfamiliaris", dbFile=db)
- cfGenome.createGeneDB(db)
-
-
-def createDBindices(db):
+def loadChromosome(db, chromID, chromPath, chromOut):
+ seqArray = []
cfGenome = Genome("cfamiliaris", dbFile=db)
- cfGenome.createIndices()
-
-
-def buildDogDB(db=geneDB):
- genePath = "%s/download/seq_gene.md" % cisRoot
- chromos = {"1": "%s/download/chr1.fa" % cisRoot,
- "2": "%s/download/chr2.fa" % cisRoot,
- "3": "%s/download/chr3.fa" % cisRoot,
- "4": "%s/download/chr4.fa" % cisRoot,
- "5": "%s/download/chr5.fa" % cisRoot,
- "6": "%s/download/chr6.fa" % cisRoot,
- "7": "%s/download/chr7.fa" % cisRoot,
- "8": "%s/download/chr8.fa" % cisRoot,
- "9": "%s/download/chr9.fa" % cisRoot,
- "10": "%s/download/chr10.fa" % cisRoot,
- "11": "%s/download/chr11.fa" % cisRoot,
- "12": "%s/download/chr12.fa" % cisRoot,
- "13": "%s/download/chr13.fa" % cisRoot,
- "14": "%s/download/chr14.fa" % cisRoot,
- "15": "%s/download/chr15.fa" % cisRoot,
- "16": "%s/download/chr16.fa" % cisRoot,
- "17": "%s/download/chr17.fa" % cisRoot,
- "18": "%s/download/chr18.fa" % cisRoot,
- "19": "%s/download/chr19.fa" % cisRoot,
- "20": "%s/download/chr20.fa" % cisRoot,
- "21": "%s/download/chr21.fa" % cisRoot,
- "22": "%s/download/chr22.fa" % cisRoot,
- '23': "%s/download/chr23.fa" % cisRoot,
- "24": "%s/download/chr24.fa" % cisRoot,
- "25": "%s/download/chr25.fa" % cisRoot,
- "26": "%s/download/chr26.fa" % cisRoot,
- "27": "%s/download/chr27.fa" % cisRoot,
- "28": "%s/download/chr28.fa" % cisRoot,
- "29": "%s/download/chr29.fa" % cisRoot,
- "30": "%s/download/chr30.fa" % cisRoot,
- "31": "%s/download/chr31.fa" % cisRoot,
- "32": "%s/download/chr32.fa" % cisRoot,
- "33": "%s/download/chr33.fa" % cisRoot,
- "34": "%s/download/chr34.fa" % cisRoot,
- "35": "%s/download/chr35.fa" % cisRoot,
- "36": "%s/download/chr36.fa" % cisRoot,
- "37": "%s/download/chr37.fa" % cisRoot,
- "38": "%s/download/chr38.fa" % cisRoot,
- "X": "%s/download/chrX.fa" % cisRoot,
- "Un": "%s/download/chrUn.fa" % cisRoot
- }
-
- print "Creating database %s" % db
- createDBFile(db)
-
- print "Adding gene entries"
- loadGeneEntries(db, genePath)
+ inFile = open(chromPath, "r")
+ line = inFile.readline()
+ for line in inFile:
+ seqArray.append(line.strip())
- print "Adding gene features"
- loadGeneFeatures(db, genePath)
+ seq = string.join(seqArray, "")
+ seqLen = len(seq)
+ if seqLen < 1:
+ print "Problems reading sequence from file"
- for chromID in chromos.keys():
- print "Loading chromosome %s" % chromID
- loadChromosome(db, chromID, chromos[chromID], "/C_familiaris/chromo%s.bin" % chromID)
+ print "writing to file %s" % chromOut
+ outFile = open("%s%s" % (cisRoot, chromOut), "w")
+ outFile.write(seq)
+ outFile.close()
+ cfGenome.addChromosomeEntry(chromID, chromOut, "file")
- print "Creating Indices"
- createDBindices(db)
- print "Finished creating database %s" % db
\ No newline at end of file
+def createDBindices(db):
+ cfGenome = Genome("cfamiliaris", dbFile=db)
+ cfGenome.createIndices()
projects / erange.git / blobdiff