###########################################################################
# #
# 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/H_sapiens/hsapiens.genedb" % cisRoot
-def loadChromosome(db, chromID, chromPath, chromOut):
- seqArray = []
- hsGenome = Genome("hsapiens", 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()
- hsGenome.addChromosomeEntry(chromID, chromOut, "file")
+def buildHsapiensDB(db=geneDB, downloadDir="%s/download" % cisRoot):
+ genePath = "%s/seq_gene.md" % downloadDir # ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/seq_gene.md.gz
+ goDefPath = "%s/GO.terms_and_ids" % downloadDir # ftp://ftp.geneontology.org/go/doc/GO.terms_and_ids
+ goPath = "%s/gene2go" % downloadDir # ftp://ftp.ncbi.nih.gov/gene/gene2go.gz
+ # chromosomes are from UCSC - will ignore all the alternative haplotypes, chrUn, and random chromosomes
+ chromList = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10",
+ "11", "12", "13", "14", "15", "16", "17", "18", "19", "20",
+ "21", "22", "X", "Y"
+ ]
+
+ print "Creating database %s" % db
+ createDBFile(db)
+
+ print "Adding gene entries"
+ loadGeneEntries(db, genePath, chromList)
+
+ print "Adding gene features"
+ loadGeneFeatures(db, genePath, chromList)
+
+ print "Adding gene annotations"
+ loadGeneAnnotations(db)
+
+ print "Adding gene ontology"
+ loadGeneOntology(db, goPath, goDefPath)
+
+ for chromID in chromList:
+ print "Loading chromosome %s" % chromID
+ chromPath = "%s/chr%s.fa" % (downloadDir, chromID)
+ loadChromosome(db, chromID, chromPath, "/H_sapiens/chromo%s.bin" % chromID)
+
+ print "Creating Indices"
+ createDBindices(db)
+
+ print "Finished creating database %s" % db
+
+
+def createDBFile(db):
+ hsGenome = Genome("hsapiens", dbFile=db)
+ hsGenome.createGeneDB(db)
def loadGeneEntries(db, gFile, cDict):
- """ FIXME - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
- """
+ #TODO: - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
geneEntries = []
hsGenome = Genome("hsapiens", dbFile=db)
geneFile = open(gFile, "r")
chrom = cols[1].strip()
if chrom not in cDict:
continue
-
+
name = cols[10].split(":")
gid = name[1]
start = int(cols[2])
cols = line.split("\t")
if cols[11] not in ["CDS", "UTR", "PSEUDO"]:
continue
+
if cols[12] == "Celera":
continue
+
chrom = cols[1].strip()
if chrom not in cDict:
continue
synonyms = idb.geneIDSynonyms(gID)
if len(synonyms) >0:
for entry in synonyms:
- gene_name += ","
+ gene_name += ","
gene_name += entry
else:
gene_name = " "
hsGenome.addGoInfoBatch(goArray)
-def createDBFile(db):
- hsGenome = Genome("hsapiens", dbFile=db)
- hsGenome.createGeneDB(db)
+def loadChromosome(db, chromID, chromPath, chromOut):
+ seqArray = []
+ hsGenome = Genome("hsapiens", 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()
+ hsGenome.addChromosomeEntry(chromID, chromOut, "file")
def createDBindices(db):
hsGenome = Genome("hsapiens", dbFile=db)
hsGenome.createIndices()
-
-
-def buildHsapiensDB(db=geneDB, downloadDir="%s/download" % cisRoot):
- genePath = "%s/seq_gene.md" % downloadDir # ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/seq_gene.md.gz
- goDefPath = "%s/GO.terms_and_ids" % downloadDir # ftp://ftp.geneontology.org/go/doc/GO.terms_and_ids
- goPath = "%s/gene2go" % downloadDir # ftp://ftp.ncbi.nih.gov/gene/gene2go.gz
- # chromosomes are from UCSC - will ignore all the alternative haplotypes, chrUn, and random chromosomes
- chromDict = {"1": "%s/chr1.fa" % downloadDir,
- "2": "%s/chr2.fa" % downloadDir,
- "3": "%s/chr3.fa" % downloadDir,
- "4": "%s/chr4.fa" % downloadDir,
- "5": "%s/chr5.fa" % downloadDir,
- "6": "%s/chr6.fa" % downloadDir,
- "7": "%s/chr7.fa" % downloadDir,
- "8": "%s/chr8.fa" % downloadDir,
- "9": "%s/chr9.fa" % downloadDir,
- "10": "%s/chr10.fa" % downloadDir,
- "11": "%s/chr11.fa" % downloadDir,
- "12": "%s/chr12.fa" % downloadDir,
- "13": "%s/chr13.fa" % downloadDir,
- "14": "%s/chr14.fa" % downloadDir,
- "15": "%s/chr15.fa" % downloadDir,
- "16": "%s/chr16.fa" % downloadDir,
- "17": "%s/chr17.fa" % downloadDir,
- "18": "%s/chr18.fa" % downloadDir,
- "19": "%s/chr19.fa" % downloadDir,
- "20": "%s/chr20.fa" % downloadDir,
- "21": "%s/chr21.fa" % downloadDir,
- "22": "%s/chr22.fa" % downloadDir,
- "X": "%s/chrX.fa" % downloadDir,
- "Y": "%s/chrY.fa" % downloadDir
- }
-
- print "Creating database %s" % db
- createDBFile(db)
-
- print "Adding gene entries"
- loadGeneEntries(db, genePath, chromDict)
-
- print "Adding gene features"
- loadGeneFeatures(db, genePath, chromDict)
-
- print "Adding gene annotations"
- loadGeneAnnotations(db)
-
- print "Adding gene ontology"
- loadGeneOntology(db, goPath, goDefPath)
-
- for chromID in chromDict.keys():
- print "Loading chromosome %s" % chromID
- loadChromosome(db, chromID, chromDict[chromID], "/H_sapiens/chromo%s.bin" % chromID)
-
- print "Creating Indices"
- createDBindices(db)
-
- print "Finished creating database %s" % db
projects / erange.git / blobdiff