###########################################################################
# #
# 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/G_gallus/ggallus.genedb" % cisRoot
-def loadChromosome(db, chromID, chromPath, chromOut):
- seqArray = []
- ggGenome = Genome("ggallus", dbFile=db)
- inFile = open(chromPath, "r")
- line = inFile.readline()
- for line in inFile:
- seqArray.append(line.strip())
+def buildChickenDB(db=geneDB):
+ genePath = "%s/download/seq_gene.md" % cisRoot
+ goDefPath = "%s/download/GO.terms_and_ids" % cisRoot # ftp://ftp.geneontology.org/pub/go/doc/GO.terms_and_ids
+ goPath = "%s/download/gene2go" % cisRoot # ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz
- 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()
- ggGenome.addChromosomeEntry(chromID, chromOut, "file")
+ print "Adding gene entries"
+ loadGeneEntries(db, genePath)
+
+ #print "Adding gene annotations"
+ #loadGeneAnnotations(db, annotPath)
+
+ 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",
+ "32", "W", "Z", "M", "E22C19W28_E50C23", "E64",
+ "1_random", "2_random", "4_random", "5_random", "6_random",
+ "7_random", "8_random", "10_random", "11_random", "12_random",
+ "13_random", "16_random", "17_random", "18_random", "20_random",
+ "22_random", "25_random", "28_random", "Un_random", "W_random",
+ "E64_random", "Z_random", "E22C19W28_E50C23_random"
+ ]
+ for chromID in chromList:
+ print "Loading chromosome %s" % chromID
+ chromPath = "%s/download/chr%s.fa" % (cisRoot, chromID)
+ loadChromosome(db, chromID, chromPath, "/G_gallus/chromo%s.bin" % chromID)
+
+ print "Adding gene ontology"
+ loadGeneOntology(db, goPath, goDefPath)
+
+ print "Creating Indices"
+ createDBindices(db)
+
+ print "Finished creating database %s" % db
+
+
+def createDBFile(db):
+ ggGenome = Genome("ggallus", dbFile=db)
+ ggGenome.createGeneDB(db)
def loadGeneEntries(db, gFile):
- """ FIXME - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
- """
+ #TODO: - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
+
geneEntries = []
alreadySeen = []
ggGenome = Genome("ggallus", dbFile=db)
ggGenome.addFeatureEntryBatch(featureEntries)
+def loadChromosome(db, chromID, chromPath, chromOut):
+ seqArray = []
+ ggGenome = Genome("ggallus", 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()
+ ggGenome.addChromosomeEntry(chromID, chromOut, "file")
+
+
def loadGeneOntology(db, goPath, goDefPath):
ggGenome = Genome("ggallus", dbFile=db)
goDefFile = open(goDefPath, "r")
ggGenome.addGoInfoBatch(goArray)
-def createDBFile(db):
- ggGenome = Genome("ggallus", dbFile=db)
- ggGenome.createGeneDB(db)
-
-
def createDBindices(db):
ggGenome = Genome("ggallus", dbFile=db)
ggGenome.createIndices()
-
-
-def buildChickenDB(db=geneDB):
- genePath = "%s/download/seq_gene.md" % cisRoot
- goDefPath = "%s/download/GO.terms_and_ids" % cisRoot # ftp://ftp.geneontology.org/pub/go/doc/GO.terms_and_ids
- goPath = "%s/download/gene2go" % cisRoot # ftp://ftp.ncbi.nih.gov/gene/DATA/gene2go.gz
- 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,
- "32": "%s/download/chr32.fa" % cisRoot,
- "W": "%s/download/chrW.fa" % cisRoot,
- "Z": "%s/download/chrZ.fa" % cisRoot,
- "M": "%s/download/chrM.fa" % cisRoot,
- "E22C19W28_E50C23": "%s/download/chrE22C19W28_E50C23.fa" % cisRoot,
- "E64": "%s/download/chrE64.fa" % cisRoot,
- "1_random": "%s/download/chr1_random.fa" % cisRoot,
- "2_random": "%s/download/chr2_random.fa" % cisRoot,
- "4_random": "%s/download/chr4_random.fa" % cisRoot,
- "5_random": "%s/download/chr5_random.fa" % cisRoot,
- "6_random": "%s/download/chr6_random.fa" % cisRoot,
- "7_random": "%s/download/chr7_random.fa" % cisRoot,
- "8_random": "%s/download/chr8_random.fa" % cisRoot,
- "10_random": "%s/download/chr10_random.fa" % cisRoot,
- "11_random": "%s/download/chr11_random.fa" % cisRoot,
- "12_random": "%s/download/chr12_random.fa" % cisRoot,
- "13_random": "%s/download/chr13_random.fa" % cisRoot,
- "16_random": "%s/download/chr16_random.fa" % cisRoot,
- "17_random": "%s/download/chr17_random.fa" % cisRoot,
- "18_random": "%s/download/chr18_random.fa" % cisRoot,
- "20_random": "%s/download/chr20_random.fa" % cisRoot,
- "22_random": "%s/download/chr22_random.fa" % cisRoot,
- "25_random": "%s/download/chr25_random.fa" % cisRoot,
- "28_random": "%s/download/chr28_random.fa" % cisRoot,
- "Un_random": "%s/download/chrUn_random.fa" % cisRoot,
- "W_random": "%s/download/chrW_random.fa" % cisRoot,
- "E64_random": "%s/download/chrE64_random.fa" % cisRoot,
- "Z_random": "%s/download/chrZ_random.fa" % cisRoot,
- "E22C19W28_E50C23_random": "%s/download/chrE22C19W28_E50C23_random.fa" % cisRoot
- }
-
- print "Creating database %s" % db
- createDBFile(db)
-
- print "Adding gene entries"
- loadGeneEntries(db, genePath)
-
- #print "Adding gene annotations"
- #loadGeneAnnotations(db, annotPath)
-
- print "Adding gene features"
- loadGeneFeatures(db, genePath)
-
- for chromID in chromos.keys():
- print "Loading chromosome %s" % chromID
- loadChromosome(db, chromID, chromos[chromID], "/G_gallus/chromo%s.bin" % chromID)
-
- print "Adding gene ontology"
- loadGeneOntology(db, goPath, goDefPath)
-
- print "Creating Indices"
- createDBindices(db)
-
- print "Finished creating database %s" % db
\ No newline at end of file
projects / erange.git / blobdiff