[med-svn] [pbsuite] 01/02: More blasr adaptations
Andreas Tille
tille at debian.org
Sat Dec 24 13:14:20 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pbsuite.
commit 8602e60d1e8510cd140fa9845cc6b2c179ac9574
Author: Andreas Tille <tille at debian.org>
Date: Sat Dec 24 13:56:37 2016 +0100
More blasr adaptations
---
debian/patches/fix_new_blasr_interface-sam.patch | 117 +++++++++++++++++++++++
debian/patches/fix_new_blasr_interface.patch | 11 +++
debian/patches/series | 1 +
3 files changed, 129 insertions(+)
diff --git a/debian/patches/fix_new_blasr_interface-sam.patch b/debian/patches/fix_new_blasr_interface-sam.patch
new file mode 100644
index 0000000..ff5ef11
--- /dev/null
+++ b/debian/patches/fix_new_blasr_interface-sam.patch
@@ -0,0 +1,117 @@
+Description: Adapt to change of command line syntax of blasr
+ There does not seem to be a real consistency in blasr options,
+ some of them are even spelled differently inside the code -
+ sometimes one '-' is used and sometimes '--' for the very same
+ option and the doc also does not seem to be up to date.
+ .
+ This patch tries the best to use the correct option spelling
+ .
+ Despite the fact that blasr documentation says '--sam' is deprecated
+ it seems to work better than only '-sam'
+ .
+ It also turned out that '-affineAlign' needs to be '--affineAlign'.
+Bug-Debian: https://bus.debian.org/844034
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
+
+--- a/pbsuite/honey/bampie.py
++++ b/pbsuite/honey/bampie.py
+@@ -11,11 +11,11 @@ from pbsuite.utils.setupLogging import s
+ #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 "
++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 "
++ "--affineAlign -affineOpen 100 -affineExtend 0 "
+ "-insertion 5 -deletion 5 -extend -maxExtendDropoff 20 "
+ "-noSplitSubreads -nCandidates 20 ")
+ #"-minPctIdentity 75 ") #didn't use this, but aybe should
+@@ -62,11 +62,11 @@ def callBlasr(inFile, refFile, params, n
+ sa = ""
+ logging.info("Running Blasr")
+ cmd = ("blasr %s %s %s --nproc %d --bestn 1 "
+- "-sam --clipping subread --out %s ") \
++ "--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 "
++ #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))
+
+--- a/pbsuite/honey/HSpots.pyx
++++ b/pbsuite/honey/HSpots.pyx
+@@ -510,7 +510,7 @@ def consensusCalling(spot, args):
+
+ #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))
+
+--- a/pbsuite/honey/Valid.py
++++ b/pbsuite/honey/Valid.py
+@@ -33,7 +33,7 @@ Main Commands:
+ mkdir level2 && cd level2
+ OLCAssembly.py ../out.fasta ../out.qual --nproc 4
+
+- blasr out.fasta ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta -sa ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta.sa --nproc 4 --out remap.sam -sam --bestn 1
++ blasr out.fasta ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta -sa ~/pacbio/data/references/human_g1k_v37/sequence/human_g1k_v37.fasta.sa --nproc 4 --out remap.sam --sam --bestn 1
+ """
+
+ VCFEntry = namedtuple("VCFEntry", "region sample haplotype")
+@@ -203,7 +203,7 @@ def remapReads( reads, outName):
+ 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
+--- a/pbsuite/honey/bakH.py
++++ b/pbsuite/honey/bakH.py
+@@ -1013,7 +1013,7 @@ class ConsensusCaller():
+
+ #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?
+
+--- a/pbsuite/honey/HSpots.py
++++ b/pbsuite/honey/HSpots.py
+@@ -205,12 +205,12 @@ def blasr(query, target, format, nproc =
+ #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")
++ "--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 @@ class ConsensusCaller():
+
+ #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))
diff --git a/debian/patches/fix_new_blasr_interface.patch b/debian/patches/fix_new_blasr_interface.patch
index 3f900d6..fc49de7 100644
--- a/debian/patches/fix_new_blasr_interface.patch
+++ b/debian/patches/fix_new_blasr_interface.patch
@@ -206,3 +206,14 @@ Last-Update: Sat, 24 Dec 2016 12:20:46 +0100
<input baseDir="/__PATH__/_TO_/jellyExample/data/reads/">
<job>filtered_subreads.fastq</job>
</input>
+--- a/pbsuite/honey/HSpots.pyx
++++ b/pbsuite/honey/HSpots.pyx
+@@ -510,7 +510,7 @@ def consensusCalling(spot, args):
+
+ #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))
+
diff --git a/debian/patches/series b/debian/patches/series
index e6d63aa..3138d3c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@ rm-intervaltree-dependency.patch
fix-example.patch
fix-shebang-lines.patch
fix_new_blasr_interface.patch
+fix_new_blasr_interface-sam.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbsuite.git
More information about the debian-med-commit
mailing list