--- /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 Caenorhaditis elegans
+import string
+from cistematic.genomes import Genome
+from os import environ
+
+if environ.get("CISTEMATIC_ROOT"):
+ cisRoot = environ.get("CISTEMATIC_ROOT")
+else:
+ cisRoot = "/proj/genome"
+
+geneDB = "%s/C_elegans/celegans.genedb" % cisRoot
+
+
+def loadChromosome(db, chromID, chromPath, chromOut):
+ seqArray = []
+ ceGenome = Genome("celegans", 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()
+ ceGenome.addChromosomeEntry(chromID, chromOut, "file")
+
+
+def loadGeneEntries(db, gffFile):
+ ceGenome = Genome("celegans", dbFile=db)
+ geneFile = open(gffFile, "r")
+ geneEntries = []
+ for line in geneFile:
+ if line[0] == "#":
+ continue
+
+ field = line.split("\t")
+ if field[1] != "Coding_transcript" and field[1] != "miRNA":
+ continue
+
+ if field[2] != "Transcript" and field[2] != "miRNA_primary_transcript":
+ continue
+
+ gidrev = field[8].split('"')
+ giddots = gidrev[1].split(".")
+ # we are ignoring gene models!!!!
+ if giddots[1][-1] in string.letters:
+ gidGene = giddots[1][:-1]
+ gidLetter = giddots[1][-1]
+ else:
+ gidGene = giddots[1]
+ gidLetter = "a"
+ gid = "%s.%s" % (giddots[0], gidGene)
+ geneID = ("celegans", gid)
+ gidVersion = 1
+ if gidLetter != "a":
+ try:
+ gidVersion = ord(gidLetter.lower()) - 96
+ except:
+ print "problem processing %s - skipping" % gidrev[1]
+ continue
+
+ start = int(field[3]) - 1
+ stop = int(field[4]) - 1
+ sense = field[6]
+ chrom = field[0].strip()
+ if sense == "+":
+ sense = "F"
+ else:
+ sense = "R"
+
+ geneEntries.append((geneID, chrom, start, stop, sense, "Transcript", gidVersion))
+
+ print "Adding %d gene entries" % len(geneEntries)
+ ceGenome.addGeneEntryBatch(geneEntries)
+
+
+def loadFeatureEntries(db, gffFile):
+ ceGenome = Genome("celegans", dbFile=db)
+ featureFile = open(gffFile, "r")
+ featureEntries = []
+ seenFeatures = {}
+ featureTranslation = {"coding_exon": "CDS",
+ "three_prime_UTR": "3UTR",
+ "five_prime_UTR": "5UTR"
+ }
+
+ for line in featureFile:
+ if line[0] == "#":
+ continue
+
+ field = line.split("\t")
+ if field[1] not in ["Coding_transcript", "miRNA", "tRNAscan-SE-1.23"]:
+ continue
+
+ if field[1] == "Coding_transcript" and field[2].strip() not in featureTranslation:
+ continue
+
+ if field[1] in ["miRNA", "tRNAscan-SE-1.23"]:
+ featureType = "CDS" # identifying these as CDS will force their masking later on
+ else:
+ featureType = featureTranslation[field[2].strip()]
+
+ gidrev = field[8].split('"')
+ giddots = gidrev[1].split(".")
+ # we are ignoring gene models!!!!
+ if giddots[1][-1] in string.letters:
+ gidGene = giddots[1][:-1]
+ gidLetter = giddots[1][-1]
+ else:
+ gidGene = giddots[1]
+ gidLetter = "a"
+
+ gid = "%s.%s" % (giddots[0], gidGene)
+ geneID = ("celegans", gid)
+ gidVersion = 1
+ if gidLetter != "a":
+ try:
+ gidVersion = ord(gidLetter.lower()) - 96
+ except:
+ print "problem processing %s - skipping" % gidrev[1]
+ continue
+
+ start = int(field[3]) - 1
+ stop = int(field[4]) - 1
+ sense = field[6]
+ chrom = field[0].strip()
+ if sense == "+":
+ sense = "F"
+ else:
+ sense = "R"
+
+ if geneID not in seenFeatures:
+ seenFeatures[geneID] = []
+
+ if (gidVersion, start, stop, featureType) not in seenFeatures[geneID]:
+ featureEntries.append((geneID, gidVersion, chrom, start, stop, sense, featureType))
+ seenFeatures[geneID].append((gidVersion, start, stop, featureType))
+
+ print "Adding %d feature entries" % len(featureEntries)
+ ceGenome.addFeatureEntryBatch(featureEntries)
+
+
+def loadGeneAnnotations(db, geneIDPath):
+ geneAnnotations = []
+ geneIDFile = open(geneIDPath, "r")
+ lines = geneIDFile.readlines()
+ geneIDFile.close()
+ ceGenome = Genome("celegans", dbFile=db)
+ for line in lines:
+ field = line.split(",")
+ try:
+ gid = field[2].strip()
+ geneID = "%s\t%s" % (field[0], field[1])
+ geneAnnotations.append((("celegans", gid), geneID))
+ except:
+ pass
+
+ print "Adding %d annotations" % len(geneAnnotations)
+ ceGenome.addAnnotationBatch(geneAnnotations)
+
+
+def loadGeneOntology(db, goPath, goDefPath, geneIDPath):
+ ceGenome = Genome("celegans", version="WS200", dbFile=db)
+ geneIDFile = open(geneIDPath, "r")
+ goDefFile = open(goDefPath, "r")
+ goFile = open(goPath, "r")
+ lines = geneIDFile.readlines()
+ geneIDFile.close()
+ geneIDmap = {}
+ seenGO = {}
+ for line in lines:
+ field = line.split(",")
+ # ugly C elegans hack - map both fields to gid, since either might be
+ # used by GO !
+ if len(field[2].strip()) > 1:
+ geneIDmap[field[1]] = field[2].strip()
+
+ goDefEntries = goDefFile.readlines()
+ goDefs = {}
+ for goDefEntry in goDefEntries:
+ if goDefEntry[0] != "!":
+ cols = goDefEntry.split("\t")
+ goDefs[cols[0]] = (cols[1], cols[2].strip())
+
+ goEntries = goFile.readlines()
+ goArray = []
+ for line in goEntries:
+ if line[0] == "!":
+ continue
+
+ fields = line.split("\t")
+ name = fields[2]
+ if name in geneIDmap:
+ name = geneIDmap[name]
+
+ if name[-1] == "a":
+ name = name[:-1]
+
+ GOIDarray = fields[4].split(" ")
+ GOID = GOIDarray[0]
+ objType = fields[8]
+ objName = fields[10].split("|")
+ gID = name
+ isNot = fields[3]
+ if len(objName) > 1:
+ name = "%s|%s" % (name.strip(), fields[10])
+
+ try:
+ GOterm = string.replace(goDefs[GOID][0], "'", "p")
+ except:
+ print "could no map %s - using GOID only" % GOID
+ GOterm = ""
+
+ evidence = fields[9]
+ if gID not in seenGO:
+ seenGO[gID] = []
+
+ if GOID not in seenGO[gID]:
+ seenGO[gID].append(GOID)
+ goArray.append((("celegans", gID), GOID, objType, name, isNot, GOterm, evidence, fields[1]))
+
+ print "Adding %d GO entries" % len(goArray)
+ ceGenome.addGoInfoBatch(goArray)
+
+
+def createDBFile(db):
+ ceGenome = Genome("celegans", version="WS200", dbFile=db)
+ ceGenome.createGeneDB(db)
+
+
+def createDBindices(db):
+ ceGenome = Genome("celegans", version="WS200", dbFile=db)
+ ceGenome.createIndices()
+
+
+def buildCelegansDB(db=geneDB, downloadRoot=""):
+ if downloadRoot == "":
+ downloadRoot = "%s/download/" % cisRoot
+
+ geneIDPath = "%sgeneIDs.WS200" % downloadRoot
+ goDefPath = "%sGO.terms_and_ids" % downloadRoot
+ goPath = "%sgene_association.wb" % downloadRoot
+
+ # can be found at ftp://caltech.wormbase.org/pub/schwarz/cisreg/softmasks
+ chromos = {"I": "%sCHROMOSOME_I_softmasked.dna" % downloadRoot,
+ "II": "%sCHROMOSOME_II_softmasked.dna" % downloadRoot,
+ "III": "%sCHROMOSOME_III_softmasked.dna" % downloadRoot,
+ "IV": "%sCHROMOSOME_IV_softmasked.dna" % downloadRoot,
+ "V": "%sCHROMOSOME_V_softmasked.dna" % downloadRoot,
+ "X": "%sCHROMOSOME_X_softmasked.dna" % downloadRoot
+ }
+
+ # can be found at ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome_feature_tables/GFF2/elegansWS160.gff.gz
+ gffPath = "%selegansWS200.gff" % downloadRoot
+
+ print "Creating database %s" % db
+ createDBFile(db)
+
+ print "Adding gene entries"
+ loadGeneEntries(db, gffPath)
+
+ print "Adding feature entries"
+ loadFeatureEntries(db, gffPath)
+
+ print "Adding gene annotations"
+ loadGeneAnnotations(db, geneIDPath)
+
+ print "Adding gene ontology"
+ loadGeneOntology(db, goPath, goDefPath, geneIDPath)
+
+ for chromID in chromos:
+ print "Loading chromosome %s" % chromID
+ loadChromosome(db, chromID, chromos[chromID], "/C_elegans/chr%s.bin" % chromID)
+
+ print "Creating Indices"
+ createDBindices(db)
+
+ print "Finished creating database %s" % db
\ No newline at end of file
projects / erange.git / blobdiff