Description: Update interface to blasr 5 blasr 5.1 and up began following the GNU convention for command-line flags. Author: Afif Elghraoui Bug: https://sourceforge.net/p/pb-jelly/tickets/5/ Bug-Debian: https://bugs.debian.org/844034 Last-Update: 2016-12-11 --- pbsuite.orig/docs/TemplateProtocol.xml +++ pbsuite/docs/TemplateProtocol.xml @@ -6,7 +6,7 @@ echo '${CMD}' | msub -N "${JOBNAME}" -o ${STDOUT} -e ${STDERR} -l nodes=1:ppn=8,mem=48000mb 1 - -minMatch 8 -sdpTupleSize 8 -minPctIdentity 75 -bestn 1 -nCandidates 10 -maxScore -500 -nproc 8 -noSplitSubreads + --minMatch 8 --sdpTupleSize 8 --minPctIdentity 75 --bestn 1 --nCandidates 10 --maxScore -500 --nproc 8 --noSplitSubreads pacbioReads.fasta --- pbsuite.orig/docs/jellyExample/Protocol.xml +++ pbsuite/docs/jellyExample/Protocol.xml @@ -1,7 +1,7 @@ /__PATH__/_TO_/jellyExample/data/reference/lambda.fasta /__PATH__/_TO_/jellyExample/ - -minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 4 -noSplitSubreads + --minMatch 8 --minPctIdentity 70 --bestn 1 --nCandidates 20 --maxScore -500 --nproc 4 --noSplitSubreads filtered_subreads.fastq --- pbsuite.orig/pbsuite/banana/chunkyBlasr.py +++ pbsuite/pbsuite/banana/chunkyBlasr.py @@ -10,10 +10,10 @@ #These are your default blasr parameters. Adjust at will. -parameters = "-maxScore -1000 -bestn 24 -maxLCPLength 16 -nCandidates 24 -noSplitSubreads" +parameters = "--maxScore -1000 --bestn 24 --maxLCPLength 16 --nCandidates 24 --noSplitSubreads" -command = Template("blasr ${FAS} ${REF} ${SA} -m 4 -out ${OUT} -start ${START} -stride ${STRIDE} ${EXTRAPARAMS}") +command = Template("blasr ${FAS} ${REF} ${SA} -m 4 --out ${OUT} --start ${START} --stride ${STRIDE} ${EXTRAPARAMS}") USAGE="""%prog --output [ ] Creates All vs All alignment of reads.fasta --- pbsuite.orig/pbsuite/banana/Banana.py +++ pbsuite/pbsuite/banana/Banana.py @@ -23,8 +23,8 @@ """ Simple overlapper """ - r,o,e = exe(("blasr %s %s -m 5 -bestn 200 -nCandidates 200 -minMatch 12 " - "-affineExtend 3 -nproc %d -noSplitSubreads -out %s -maxScore -1000") % \ + r,o,e = exe(("blasr %s %s -m 5 --bestn 200 --nCandidates 200 --minMatch 12 " + "--affineExtend 3 --nproc %d --noSplitSubreads --out %s --maxScore -1000") % \ (query, target, nproc, outname)) def m5ToOvlGraph(readNames, fileName): --- pbsuite.orig/pbsuite/banana/Polish.py +++ pbsuite/pbsuite/banana/Polish.py @@ -17,7 +17,7 @@ """ runs blasr """ - r,o,e = exe("blasr %s %s -bestn %d -affineAlign -m 5 -nproc %d -out %s" \ + r,o,e = exe("blasr %s %s --bestn %d --affineAlign -m 5 --nproc %d --out %s" \ % (query, target, bestn, nproc, outName)) --- pbsuite.orig/pbsuite/banana/OLCAssembly.py +++ pbsuite/pbsuite/banana/OLCAssembly.py @@ -158,9 +158,9 @@ Takes all of the pools and generates their fastq and alignments in their own folder. """ logging.info("Creating Overlap") - log = _exe(("blasr inputReads.fastq reference.fasta -nproc %d -m 4 " - "-out temp.rm4 -noSplitSubreads -useGuidedAlign -allowAdjacentIndels "#-minFrac 0.01 - "-nCandidates 20 -bestn 15 -minMatch 8 -maxLCPLength 16 ") % (self.options.nproc) ) + log = _exe(("blasr inputReads.fastq reference.fasta --nproc %d -m 4 " + "--out temp.rm4 --noSplitSubreads --useGuidedAlign --allowAdjacentIndels "#-minFrac 0.01 + "--nCandidates 20 --bestn 15 --minMatch 8 --maxLCPLength 16 ") % (self.options.nproc) ) logging.debug(log) logging.info("Sorting the alignments") logging.debug(_exe("sort temp.rm4 > alignments.rm4")) --- pbsuite.orig/pbsuite/jelly/QFix.py +++ pbsuite/pbsuite/jelly/QFix.py @@ -16,7 +16,7 @@ fout.write(">%s\n%s\n" % (i.name, i.seq)) fout.close() - print exe(("blasr input.fastq ref.fasta -bestn 2 -m 5 -noSplitSubreads > out.m5")) + print exe(("blasr input.fastq ref.fasta --bestn 2 -m 5 --noSplitSubreads > out.m5")) print exe(("python /stornext/snfs5/next-gen/scratch/english/Jelly/" "DevJelly/branches/consensusDev/GetSubs.py out.m5 input.fastq")) print exe(("python /stornext/snfs5/next-gen/scratch/english/Jelly/" --- pbsuite.orig/pbsuite/jelly/Stages.py +++ pbsuite/pbsuite/jelly/Stages.py @@ -56,7 +56,7 @@ logging.basicConfig( stream=sys.stderr, level=level, format=logFormat ) logging.info("Running blasr") - mappingTemplate = Template("blasr ${fasta} ${ref} ${sa} -m 4 -out ${outFile} ${parameters} ") + mappingTemplate = Template("blasr ${fasta} ${ref} ${sa} -m 4 --out ${outFile} ${parameters} ") tailTemplate = Template("m4pie.py ${outFile} ${fasta} ${ref} --nproc ${nproc} -i ${extras}") ret = [] @@ -79,7 +79,7 @@ logging.warning("Output File %s already exists and will be overwritten." % (outFile)) #Build Blasr Command - nprocRe = re.compile("-nproc (\d+)") + nprocRe = re.compile("--nproc (\d+)") np = nprocRe.findall(parameters + extras) if len(np) == 0: np = '1' --- pbsuite.orig/pbsuite/jelly/Assembly.py +++ pbsuite/pbsuite/jelly/Assembly.py @@ -18,8 +18,8 @@ """ Simple overlapper """ - c = ("blasr %s %s -m %s -bestn %d -nCandidates %d -minMatch 8 -sdpTupleSize 6 -affineAlign " - "-nproc %d -noSplitSubreads -out %s -minPctIdentity 60 -minReadLength 5") % \ + c = ("blasr %s %s -m %s --bestn %d --nCandidates %d --minMatch 8 --sdpTupleSize 6 --affineAlign " + "--nproc %d --noSplitSubreads --out %s --minPctIdentity 60 --minReadLength 5") % \ (query, target, fmt, bestn, nCandidates, nproc, outname) logging.debug(c) r,o,e = exe(c) --- pbsuite.orig/pbsuite/jelly/m4pie.py +++ pbsuite/pbsuite/jelly/m4pie.py @@ -75,8 +75,8 @@ sa = "-sa " + ref + ".sa" else: sa = "" - cmd = ("blasr %s %s %s -nproc %d -m 4 -bestn 1 -nCandidates 20 -out %s" - " -minPctIdentity 75 -sdpTupleSize 6 -noSplitSubreads") \ + cmd = ("blasr %s %s %s --nproc %d -m 4 --bestn 1 --nCandidates 20 --out %s" + " --minPctIdentity 75 --sdpTupleSize 6 --noSplitSubreads") \ % (fq, ref, sa, nproc, out) logging.debug(cmd) --- pbsuite.orig/pbsuite/honey/HSpots.pyx +++ pbsuite/pbsuite/honey/HSpots.pyx @@ -510,7 +510,7 @@ #map consensus to refregion varSam = NamedTemporaryFile(suffix=".sam") - cmd = "blasr %s %s -sam -bestn 1 -affineAlign -out %s" % (conOut.name, refOut.name, varSam.name) + cmd = "blasr %s %s --sam --bestn 1 --affineAlign --out %s" % (conOut.name, refOut.name, varSam.name) logging.debug(cmd) logging.debug(exe(cmd)) --- pbsuite.orig/pbsuite/honey/HSpots.py +++ pbsuite/pbsuite/honey/HSpots.py @@ -200,17 +200,17 @@ """ Simple mapper """ - cmd = ("blasr %s %s %s -nproc %d -bestn 1 -out %s ") \ + cmd = ("blasr %s %s %s --nproc %d --bestn 1 --out %s ") \ % (query, target, format, nproc, outname) #need to figure out how to m5-pie it...maybe if consensus: - r, o, e = exe(cmd + " -noSplitSubreads -minMatch 5 " + \ - "-nCandidates 20 -sdpTupleSize 6 -insertion 1 -deletion 1 -bestn 1") + r, o, e = exe(cmd + " --noSplitSubreads --minMatch 5 " + \ + "--nCandidates 20 --sdpTupleSize 6 --insertion 1 --deletion 1 --bestn 1") else: - r, o, e = exe(cmd + " -maxAnchorsPerPosition 100 " - "-affineAlign -affineOpen 100 -affineExtend 0 " - "-insertion 10 -deletion 10 " - "-noSplitSubreads -nCandidates 20 ") + r, o, e = exe(cmd + " --maxAnchorsPerPosition 100 " + "--affineAlign --affineOpen 100 --affineExtend 0 " + "--insertion 10 --deletion 10 " + "--noSplitSubreads --nCandidates 20 ") logging.debug("blasr - %d - %s - %s" % (r, o, e)) @@ -1000,7 +1000,7 @@ #map consensus to refregion varSam = NamedTemporaryFile(suffix=".sam") - blasr(conOut.name, refOut.name, format="-sam", outname=varSam.name,\ + blasr(conOut.name, refOut.name, format="--sam", outname=varSam.name,\ consensus=False) #-- would this help? #or what if I fed it through leftalign? #os.system("cp %s ." % (refOut.name)) --- pbsuite.orig/pbsuite/honey/bakH.py +++ pbsuite/pbsuite/honey/bakH.py @@ -187,7 +187,7 @@ """ Simple mapper """ - cmd = ("blasr %s %s %s -nproc %d -bestn 1 -out %s ") \ + cmd = ("blasr %s %s %s --nproc %d --bestn 1 --out %s ") \ % (query, target, format, nproc, outname) #need to figure out how to m5-pie it...maybe if consensus: @@ -1013,7 +1013,7 @@ #map consensus to refregion varSam = NamedTemporaryFile(suffix=".sam") - blasr(conOut.name, refOut.name, format="-sam", outname=varSam.name) + blasr(conOut.name, refOut.name, format="--sam", outname=varSam.name) #consensus=False) -- would this help? #or what if I fed it through leftalign? --- pbsuite.orig/pbsuite/honey/bampie.py +++ pbsuite/pbsuite/honey/bampie.py @@ -11,14 +11,14 @@ #Edit this string to set which parameters blasr will use by default #DO NOT! Set -nproc, -bestn, -clipping, or any output (e.g. -out -m 5) #Remove -noSpotSubreads if your inputs are bax.h5 files [i think] -BLASRPARAMS = (" -affineAlign -noSplitSubreads -nCandidates 20 " - "-minPctIdentity 75 -sdpTupleSize 6") +BLASRPARAMS = (" --affineAlign --noSplitSubreads --nCandidates 20 " + "--minPctIdentity 75 --sdpTupleSize 6") #Parameters used in the eichler experiments -EEBLASRPARAMS = (" -maxAnchorsPerPosition 100 -advanceExactMatches 10 " - "-affineAlign -affineOpen 100 -affineExtend 0 " - "-insertion 5 -deletion 5 -extend -maxExtendDropoff 20 " - "-noSplitSubreads -nCandidates 20 ") - #"-minPctIdentity 75 ") #didn't use this, but aybe should +EEBLASRPARAMS = (" --maxAnchorsPerPosition 100 --advanceExactMatches 10 " + "--affineAlign --affineOpen 100 --affineExtend 0 " + "--insertion 5 --deletion 5 --extend --maxExtendDropoff 20 " + "--noSplitSubreads --nCandidates 20 ") + #"--minPctIdentity 75 ") #didn't use this, but aybe should #have @@ -42,9 +42,9 @@ """ def checkBlasrParams(bp): """ - Ensure -bestn, -nproc, -clipping, -out are not specified + Ensure --bestn, --nproc, --clipping, --out are not specified """ - args = [" -bestn ", " -nproc ", " -clipping ", " -out ", " -m "] + args = [" --bestn ", " --nproc ", " --clipping ", " --out ", " -m "] for i in args: if bp.count(i): logging.error("Do not specify %s through Honey.py pie" % (i)) @@ -57,18 +57,18 @@ automatically search for .sa """ if os.path.exists(refFile+".sa"): - sa = "-sa " + refFile + ".sa" + sa = "--sa " + refFile + ".sa" else: sa = "" logging.info("Running Blasr") - cmd = ("blasr %s %s %s -nproc %d -bestn 1 " - "-sam -clipping subread -out %s ") \ + cmd = ("blasr %s %s %s --nproc %d --bestn 1 " + "--sam --clipping subread --out %s ") \ % (inFile, refFile, sa, nproc, outFile) r, o, e = exe(cmd + params) - #r,o,e = exe(("blasr %s %s %s -nproc %d -sam -bestn 1 -nCandidates 20 " - #"-out %s -clipping soft -minPctIdentity 75 " - #" -noSplitSubreads") % (fq, ref, sa, nproc, out)) + #r,o,e = exe(("blasr %s %s %s --nproc %d --sam --bestn 1 --nCandidates 20 " + #"--out %s --clipping soft --minPctIdentity 75 " + #" --noSplitSubreads") % (fq, ref, sa, nproc, out)) if r != 0: logging.error("blasr mapping failed!") --- pbsuite.orig/pbsuite/honey/Valid.py +++ pbsuite/pbsuite/honey/Valid.py @@ -203,7 +203,7 @@ remaps reads to the provided reference (only setup for hg19 -- see global variable reference) """ - return exe("blasr {0} {1} -sa {1}.sa -nproc 4 -out {2} -sam -bestn 1"\ + return exe("blasr {0} {1} --sa {1}.sa --nproc 4 --out {2} --sam --bestn 1"\ .format(reads, reference, outName)) @exeLog