--- /dev/null
+import sys
+import optparse
+import ReadDataset
+from commoncode import writeLog
+from checkrmask import checkrmask
+from geneMrnaCounts import geneMrnaCounts
+from geneMrnaCountsWeighted import geneMrnaCountsWeighted
+from getallgenes import getallgenes
+from normalizeFinalExonic import normalizeFinalExonic
+from normalizeExpandedExonic import normalizeExpandedExonic
+from findall import findall, RegionFinder
+
+VERSION = "1.0"
+
+def main(argv=None):
+ if not argv:
+ argv = sys.argv
+
+ print "runStrandedAnalysis: version %s" % VERSION
+ usage = "usage: python runStrandedAnalysis.py genome rdsprefix repeatmaskdb bpradius"
+
+ parser = getParser(usage)
+ (options, args) = parser.parse_args(argv[1:])
+
+ if len(args) < 4:
+ print usage
+ sys.exit(1)
+
+ genome = args[0]
+ rdsprefix = args[1]
+ repeatmaskdb = args[2]
+ bpradius = args[3]
+
+ runStrandedAnalysis(genome, rdsprefix, repeatmaskdb, bpradius)
+
+
+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+
+ return parser
+
+
+def runStrandedAnalysis(genome, rdsprefix, repeatmaskdb, bpradius):
+ """ based on original script runStrandedAnalysis.sh
+ usage: runStrandedAnalysis.sh genome rdsprefix repeatmaskdb bpradius
+ where rdsprefix is the name of the rds file without the .rds extension
+ use "none" for the repeatmaskdb if you do not have one
+ """
+
+ rdsfile = "%s.rds" % rdsprefix
+ logfile = "rna.log"
+
+ # log the parameters
+ message = "with parameters: %s %s %s %s" % (genome, rdsprefix, repeatmaskdb, bpradius)
+ writeLog(logfile, "runStrandedAnalysis.py", message)
+
+ # count the unique reads falling on the gene models ; the nomatch files are
+ # mappable reads that fell outside of the Cistematic gene models and not the
+ # unmappable of Eland (i.e, the "NM" reads)
+ uniquecountfilename = "%s.uniqs.count" % rdsprefix
+ geneMrnaCounts(genome, rdsfile, uniquecountfilename, trackStrand=True, cachePages=1, markGID=True)
+
+ # calculate a first-pass RPKM to re-weigh the unique reads,
+ # using 'none' for the splice count
+ initialrpkmfilename = "%s.firstpass.rpkm" % rdsprefix
+ RDS = ReadDataset.ReadDataset(rdsfile, verbose=True, cache=True, reportCount=False)
+ (ucount, mcount, scount) = RDS.getCounts(multi=True, splices=True, reportCombined=False)
+ readCounts = {}
+ readCounts["uniq"] = ucount
+ readCounts["splice"] = mcount
+ readCounts["multi"] = scount
+ normalizeExpandedExonic(genome, readCounts["uniq"], uniquecountfilename, "none", initialrpkmfilename, doCache=True)
+
+ # recount the unique reads with weights calculated during the first pass
+ initialrpkmfilename = "%s.firstpass.rpkm" % rdsprefix
+ uniquerecountfilename = "%s.uniqs.recount" % rdsprefix
+ geneMrnaCountsWeighted(genome, rdsfile, initialrpkmfilename, uniquerecountfilename, withUniqs=True, cachePages=1, ignoreSense=False)
+
+ # count splice reads
+ splicecountfilename = "%s.splices.count" % rdsprefix
+ geneMrnaCounts(genome, rdsfile, splicecountfilename, trackStrand=True, doSplices=True, doUniqs=False, cachePages=1)
+
+ # find new regions outside of gene models with reads piled up
+ newregionfilename = "%s.newregions.txt" % rdsprefix
+ regionFinder = RegionFinder("RNAFARP", minHits=1, withFlag="NM", strandfilter="plus")
+ findall(regionFinder, rdsfile, newregionfilename, logfilename=logfile, rnaSettings=True, cachePages=1, useMulti=False)
+
+ regionFinder = RegionFinder("RNAFARM", minHits=1, withFlag="NM", strandfilter="plus")
+ findall(regionFinder, rdsfile, newregionfilename, logfilename=logfile, rnaSettings=True, cachePages=1, useMulti=False, outputMode="a")
+
+ # filter out new regions that overlap repeats more than a certain fraction
+ newregionfilename = "%s.newregions.txt" % rdsprefix
+ outFileName = "%s.newregions.repstatus" % rdsprefix
+ goodFileName = "%s.newregions.good" % rdsprefix
+ checkrmask(repeatmaskdb, newregionfilename, outFileName, goodFileName, startField=1, cachePages=1, logfilename=logfile)
+
+ #TODO: these calls look wrong
+ # Alternative 2: use a precomputed list of "new" regions (outside of gene models)
+ #python $ERANGEPATH/regionCounts.py $3 $2.nomatch.bed $2.newregions.good $2.stillnomatch.bed
+ #python $ERANGEPATH/regionCounts.py $3 $2.rds $2.newregions.good
+
+ # map all candidate regions that are within a given radius of a gene in bp
+ candidatefilename = "%s.candidates.txt" % rdsprefix
+ getallgenes(genome, goodFileName, candidatefilename, maxRadius=bpradius, trackFar=True, doCache=True, trackStrand=True)
+
+ expandedRPKMfilename = "%s.expanded.rpkm" % rdsprefix
+ # calculate expanded exonic read density
+ acceptedfilename = "%s.accepted.rpkm" % rdsprefix
+ try:
+ candidatefile = open(candidatefilename)
+ candidateLines = candidatefile.readlines()
+ candidatefile.close()
+ except IOError:
+ candidateLines = []
+
+ normalizeExpandedExonic(genome, readCounts["uniq"], uniquerecountfilename, splicecountfilename, expandedRPKMfilename, candidateLines=candidateLines, acceptedfilename=acceptedfilename,
+ doCache=True)
+
+ # weigh multi-reads
+ multicountfilename = "%s.multi.count" % rdsprefix
+ geneMrnaCountsWeighted(genome, rdsfile, expandedRPKMfilename, multicountfilename, withMulti=True, acceptfile=acceptedfilename, cachePages=1)
+
+ # calculate final exonic read density
+ outfilename = "%s.final.rpkm" % rdsprefix
+ normalizeFinalExonic(readCounts, expandedRPKMfilename, multicountfilename, outfilename, reportFraction=True, doCache=True, writeGID=True)
+
+
+if __name__ == "__main__":
+ main(sys.argv)
\ No newline at end of file
projects / erange.git / blobdiff