--- /dev/null
+###########################################################################
+# #
+# C O P Y R I G H T N O T I C E #
+# Copyright (c) 2003-10 by: #
+# * California Institute of Technology #
+# #
+# All Rights Reserved. #
+# #
+# Permission is hereby granted, free of charge, to any person #
+# obtaining a copy of this software and associated documentation files #
+# (the "Software"), to deal in the Software without restriction, #
+# including without limitation the rights to use, copy, modify, merge, #
+# publish, distribute, sublicense, and/or sell copies of the Software, #
+# and to permit persons to whom the Software is furnished to do so, #
+# subject to the following conditions: #
+# #
+# The above copyright notice and this permission notice shall be #
+# included in all copies or substantial portions of the Software. #
+# #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, #
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF #
+# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND #
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS #
+# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN #
+# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN #
+# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE #
+# SOFTWARE. #
+###########################################################################
+#
+# data for Gallus gallus
+import string
+from cistematic.genomes import Genome
+from cistematic.core.geneinfo import geneinfoDB
+from os import environ
+
+if 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())
+
+ 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 loadGeneEntries(db, gFile):
+ """ FIXME - NEED TO DEAL WITH ALTERNATIVE SPLICING ENTRIES
+ """
+ geneEntries = []
+ alreadySeen = []
+ ggGenome = Genome("ggallus", dbFile=db)
+ geneFile = open(gFile, "r")
+ geneFile.readline()
+ for line in geneFile:
+ if "|" in line:
+ continue
+
+ cols = line.split("\t")
+ if cols[11].strip() != "GENE":
+ continue
+
+ name = cols[10].split(":")
+ gid = name[1]
+ if gid == "" or gid in alreadySeen:
+ continue
+
+ alreadySeen.append(gid)
+ start = int(cols[2]) - 1
+ stop = int(cols[3]) - 1
+ sense = cols[4]
+ chrom = cols[1].strip()
+ if sense == "+":
+ sense = "F"
+ else:
+ sense = "R"
+
+ geneID = ("ggallus", gid)
+ gidVersion = 1
+ geneEntries.append((geneID, chrom, start, stop, sense, "gene", gidVersion))
+
+ print "Adding %d gene entries" % len(geneEntries)
+ ggGenome.addGeneEntryBatch(geneEntries)
+
+
+def loadGeneFeatures(db, gFile):
+ """ Load gene features such as CDS, UTR, and PSEUDO from the gene file.
+ """
+ featureEntries = []
+ ggGenome = Genome("ggallus", dbFile=db)
+ featureFile = open(gFile, "r")
+ featureFile.readline()
+ for line in featureFile:
+ if "|" in line:
+ continue
+
+ cols = line.split("\t")
+ if cols[11].strip() not in ["CDS", "UTR", "PSEUDO"]:
+ continue
+
+ fType = cols[11]
+ name = cols[10].split(":")
+ gid = name[1]
+ if gid == "":
+ continue
+
+ start = int(cols[2]) - 1
+ stop = int(cols[3]) - 1
+ sense = cols[4]
+ chrom = cols[1].strip()
+ if sense == "+":
+ sense = "F"
+ else:
+ sense = "R"
+
+ geneID = ("ggallus", gid)
+ gidVersion = 1
+ featureEntries.append((geneID, gidVersion, chrom, start, stop, sense, fType))
+
+ print "Adding %d feature entries" % len(featureEntries)
+ ggGenome.addFeatureEntryBatch(featureEntries)
+
+
+def loadGeneOntology(db, goPath, goDefPath):
+ ggGenome = Genome("ggallus", dbFile=db)
+ goDefFile = open(goDefPath, "r")
+ goFile = open(goPath, "r")
+ idb = geneinfoDB()
+ goDefs = {}
+ goArray = []
+ for goDefEntry in goDefFile:
+ if goDefEntry[0] != "!":
+ cols = goDefEntry.split("\t")
+ goDefs[cols[0]] = (cols[1], cols[2].strip())
+
+ goEntries = goFile.readlines()
+ prevGID = ""
+ for entry in goEntries:
+ try:
+ fields = entry.split("\t")
+ if fields[0] != "9031":
+ continue
+
+ locID = fields[1].strip()
+ gID = ("ggallus", locID)
+ if prevGID != gID:
+ prevGID = gID
+ gene_name = ""
+ synonyms = idb.geneIDSynonyms(gID)
+ if len(synonyms) >0:
+ gene_name = string.join(synonyms, ",")
+
+ goArray.append((gID, fields[2], "", gene_name, "", string.replace(goDefs[fields[2]][0], "'", "p"), goDefs[fields[2]][1], ""))
+ except:
+ print "locus ID %s could not be added" % locID
+ pass
+
+ print "adding %d go entries" % len(goArray)
+ 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