[med-svn] [pbsuite] 01/01: WIP: Update pbhoney to blasr 5 interface
Afif Elghraoui
afif at moszumanska.debian.org
Sun Dec 11 22:09:03 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch topic/blasr5
in repository pbsuite.
commit 5832c4fea5f60437864cf75a828ab3d60efbbc63
Author: Afif Elghraoui <afif at debian.org>
Date: Sun Dec 11 14:05:10 2016 -0800
WIP: Update pbhoney to blasr 5 interface
blasr's interface changed in version 5.1. Blasr has no changelog,
but there is a sort of changelog in the blasr source (Blasr.cpp)
that indicates the change happened at v5.1.
Before this patch can be properly tested, blasr in Debian needs to be
built with pbbam (to allow use of the --sam flag that the pbsuite
needs).
Closes: #844034
---
debian/control | 4 +-
debian/patches/blasr-5.patch | 279 +++++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
3 files changed, 282 insertions(+), 2 deletions(-)
diff --git a/debian/control b/debian/control
index 6b41c64..49acc61 100644
--- a/debian/control
+++ b/debian/control
@@ -49,7 +49,7 @@ Depends:
${python:Depends},
python-pbsuite-utils (= ${source:Version}),
python-networkx,
- blasr,
+ blasr (>= 5.1),
Description: genome assembly upgrading tool
PBJelly is a highly automated pipeline that aligns long sequencing
reads (such as PacBio RS reads or long 454 reads in fasta format)
@@ -69,7 +69,7 @@ Depends:
python-networkx,
python-h5py (>= 2.0.1),
python-numpy,
- blasr,
+ blasr (>= 5.1),
samtools,
Recommends:
pbdagcon,
diff --git a/debian/patches/blasr-5.patch b/debian/patches/blasr-5.patch
new file mode 100644
index 0000000..e2d5fab
--- /dev/null
+++ b/debian/patches/blasr-5.patch
@@ -0,0 +1,279 @@
+Description: Update interface to blasr 5
+ blasr 5.1 and up began following the GNU convention for command-line flags.
+Author: Afif Elghraoui <afif at debian.org>
+Bug: https://sourceforge.net/p/pb-jelly/tickets/5/
+Bug-Debian: https://bugs.debian.org/844034
+Forwarded: no
+Last-Update: 2016-12-11
+--- pbsuite.orig/docs/TemplateProtocol.xml
++++ pbsuite/docs/TemplateProtocol.xml
+@@ -6,7 +6,7 @@
+ <command notes="For PBS/Moab">echo '${CMD}' | msub -N "${JOBNAME}" -o ${STDOUT} -e ${STDERR} -l nodes=1:ppn=8,mem=48000mb</command>
+ <nJobs>1</nJobs>
+ </cluster>
+- <blasr>-minMatch 8 -sdpTupleSize 8 -minPctIdentity 75 -bestn 1 -nCandidates 10 -maxScore -500 -nproc 8 -noSplitSubreads</blasr>
++ <blasr>--minMatch 8 --sdpTupleSize 8 --minPctIdentity 75 --bestn 1 --nCandidates 10 --maxScore -500 --nproc 8 --noSplitSubreads</blasr>
+ <input baseDir="/FULL/PATH/TO__/PBJelly/lambdaExample/data/reads/">
+ <job>pacbioReads.fasta</job>
+ </input>
+--- pbsuite.orig/docs/jellyExample/Protocol.xml
++++ pbsuite/docs/jellyExample/Protocol.xml
+@@ -1,7 +1,7 @@
+ <jellyProtocol>
+ <reference>/__PATH__/_TO_/jellyExample/data/reference/lambda.fasta</reference>
+ <outputDir>/__PATH__/_TO_/jellyExample/</outputDir>
+- <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 4 -noSplitSubreads</blasr>
++ <blasr>--minMatch 8 --minPctIdentity 70 --bestn 1 --nCandidates 20 --maxScore -500 --nproc 4 --noSplitSubreads</blasr>
+ <input baseDir="/__PATH__/_TO_/jellyExample/data/reads/">
+ <job>filtered_subreads.fastq</job>
+ </input>
+--- 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 <reads.fasta> --output <outName> [ <options> ]
+ 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
diff --git a/debian/patches/series b/debian/patches/series
index 3435ec7..7598597 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ intervaltree-import-statement.patch
rm-intervaltree-dependency.patch
fix-example.patch
fix-shebang-lines.patch
+blasr-5.patch
--
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