X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=erange.git;a=blobdiff_plain;f=runStrandedAnalysis.py;fp=runStrandedAnalysis.py;h=35a67008d196ea0c942e2fb94614a7e76f612f7e;hp=55c87ca76e48a1e272bf1184ec6fd3bd5ff9b1e9;hb=4ad5495359e4322da39868020a7398676261679e;hpb=cfc5602b26323ad2365295145e3f6c622d912eb4

diff --git a/runStrandedAnalysis.py b/runStrandedAnalysis.py
index 55c87ca..35a6700 100644
--- a/runStrandedAnalysis.py
+++ b/runStrandedAnalysis.py
@@ -1,7 +1,7 @@
 import sys
 import optparse
-import ReadDataset
-from commoncode import writeLog
+import pysam
+from commoncode import writeLog, getHeaderComment
 from checkrmask import checkrmask
 from geneMrnaCounts import geneMrnaCounts
 from geneMrnaCountsWeighted import geneMrnaCountsWeighted
@@ -40,58 +40,57 @@ def getParser(usage):
     return parser
 
 
-def runStrandedAnalysis(genome, rdsprefix, repeatmaskdb, bpradius):
+def runStrandedAnalysis(genome, fileprefix, 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
+    bamfilename = "%s.bam" % fileprefix
+    bamfile = pysam.Samfile(bamfilename, "rb")
     logfile = "rna.log"
 
     # log the parameters
-    message = "with parameters: %s %s %s %s" % (genome, rdsprefix, repeatmaskdb, bpradius)
+    message = "with parameters: %s %s %s %s" % (genome, fileprefix, 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)
+    uniquecountfilename = "%s.uniqs.count" % fileprefix
+    geneMrnaCounts(genome, bamfile, uniquecountfilename, trackStrand=True, 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)
+    initialrpkmfilename = "%s.firstpass.rpkm" % fileprefix
     readCounts = {}
-    readCounts["uniq"] = ucount
-    readCounts["splice"] = mcount
-    readCounts["multi"] = scount
+    readCounts["uniq"] = int(getHeaderComment(bamfile.header, "Unique"))
+    readCounts["splice"] = int(getHeaderComment(bamfile.header, "UniqueSplices"))
+    readCounts["multi"] = int(getHeaderComment(bamfile.header, "Multis"))
     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)
+    initialrpkmfilename = "%s.firstpass.rpkm" % fileprefix
+    uniquerecountfilename = "%s.uniqs.recount" % fileprefix
+    geneMrnaCountsWeighted(genome, bamfile, 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)
+    splicecountfilename = "%s.splices.count" % fileprefix
+    geneMrnaCounts(genome, bamfile, splicecountfilename, trackStrand=True, doSplices=True, doUniqs=False)
 
     # find new regions outside of gene models with reads piled up 
-    newregionfilename = "%s.newregions.txt" % rdsprefix
+    newregionfilename = "%s.newregions.txt" % fileprefix
     regionFinder = RegionFinder("RNAFARP", minHits=1, withFlag="NM", strandfilter="plus")
-    findall(regionFinder, rdsfile, newregionfilename, logfilename=logfile, rnaSettings=True, cachePages=1, useMulti=False)
+    findall(regionFinder, bamfilename, newregionfilename, logfilename=logfile, rnaSettings=True, 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")
+    findall(regionFinder, bamfile, newregionfilename, logfilename=logfile, rnaSettings=True, 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
+    newregionfilename = "%s.newregions.txt" % fileprefix
+    outFileName = "%s.newregions.repstatus" % fileprefix
+    goodFileName = "%s.newregions.good" % fileprefix
     checkrmask(repeatmaskdb, newregionfilename, outFileName, goodFileName, startField=1, cachePages=1, logfilename=logfile)
 
     #TODO: these calls look wrong
@@ -100,28 +99,21 @@ def runStrandedAnalysis(genome, rdsprefix, repeatmaskdb, bpradius):
     #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
+    candidatefilename = "%s.candidates.txt" % fileprefix
     getallgenes(genome, goodFileName, candidatefilename, maxRadius=bpradius, trackFar=True, doCache=True, trackStrand=True)
 
-    expandedRPKMfilename = "%s.expanded.rpkm" % rdsprefix
+    expandedRPKMfilename = "%s.expanded.rpkm" % fileprefix
     # 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)
+    acceptedfilename = "%s.accepted.rpkm" % fileprefix
+    normalizeExpandedExonic(genome, readCounts["uniq"], uniquerecountfilename, splicecountfilename, expandedRPKMfilename, candidatefilename=candidatefilename,
+                            acceptedfilename=acceptedfilename, doCache=True)
 
     # weigh multi-reads
-    multicountfilename = "%s.multi.count" % rdsprefix
-    geneMrnaCountsWeighted(genome, rdsfile, expandedRPKMfilename, multicountfilename, withMulti=True, acceptfile=acceptedfilename, cachePages=1)
+    multicountfilename = "%s.multi.count" % fileprefix
+    geneMrnaCountsWeighted(genome, bamfile, expandedRPKMfilename, multicountfilename, withMulti=True, acceptfile=acceptedfilename, cachePages=1)
 
     # calculate final exonic read density
-    outfilename = "%s.final.rpkm" % rdsprefix
+    outfilename = "%s.final.rpkm" % fileprefix
     normalizeFinalExonic(readCounts, expandedRPKMfilename, multicountfilename, outfilename, reportFraction=True, doCache=True, writeGID=True)