diff options
| -rw-r--r-- | academic/pyCRAC/GTF2-scripts.patch | 79 | ||||
| -rw-r--r-- | academic/pyCRAC/README | 8 | ||||
| -rw-r--r-- | academic/pyCRAC/pyCRAC.SlackBuild | 8 | ||||
| -rw-r--r-- | academic/pyCRAC/pyCRAC.info | 6 | ||||
| -rw-r--r-- | academic/pyCRAC/setup_slack.py | 2 |
5 files changed, 11 insertions, 92 deletions
diff --git a/academic/pyCRAC/GTF2-scripts.patch b/academic/pyCRAC/GTF2-scripts.patch deleted file mode 100644 index 35f9512876..0000000000 --- a/academic/pyCRAC/GTF2-scripts.patch +++ /dev/null @@ -1,79 +0,0 @@ -diff -Naur sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2bedGraph.py sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2bedGraph.py ---- sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2bedGraph.py 2017-09-11 15:11:12.000000000 +0100 -+++ sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2bedGraph.py 2017-09-10 00:47:13.014633000 +0100 -@@ -2,7 +2,7 @@ - # not compatible with python 3 - __author__ = "Sander Granneman" - __copyright__ = "Copyright 2017" --__version__ = "0.0.7" -+__version__ = "0.0.6" - __credits__ = ["Sander Granneman"] - __maintainer__ = "Sander Granneman" - __email__ = "sgrannem@staffmail.ed.ac.uk" -@@ -80,14 +80,12 @@ - chromdata = processChromFile(chromlengthfile) - ### - -- normvalue = 1.0 -- if permillion and normvalue == 1.0: -- assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data" -- normvalue = float(data.mapped_reads)/1000000.0 -- - while True: - lines = data.readLineByLine() -- # to normalize the data to per million reads -+ normvalue = 1.0 -+ if permillion and normvalue == 1.0: -+ assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data" -+ normvalue = float(data.mapped_reads)/1000000.0 # to normalize the data to per million reads - if current_chromosome and data.chromosome != current_chromosome or not lines: - for strand in chromdict: - start = 0 -diff -Naur sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2sgr.py sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2sgr.py ---- sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2sgr.py 2017-09-11 15:11:12.000000000 +0100 -+++ sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2sgr.py 2017-09-10 00:47:13.014633000 +0100 -@@ -1,8 +1,8 @@ - #!/usr/bin/python - # not compatible with python 3 - __author__ = "Sander Granneman" --__copyright__ = "Copyright 2017" --__version__ = "0.0.6" -+__copyright__ = "Copyright 2015" -+__version__ = "0.0.5" - __credits__ = ["Sander Granneman"] - __maintainer__ = "Sander Granneman" - __email__ = "sgrannem@staffmail.ed.ac.uk" -@@ -13,7 +13,7 @@ - # pyGTF2sgr.py - # - # --# Copyright (c) Sander Granneman 2017 -+# Copyright (c) Sander Granneman 2015 - # - # Permission is hereby granted, free of charge, to any person obtaining a copy - # of this software and associated documentation files (the "Software"), to deal -@@ -73,12 +73,11 @@ - ### - - normvalue = 1.0 -- if permillion: -- assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data" -- normvalue = float(data.mapped_reads)/1000000.0 -- - while True: - lines = data.readLineByLine() -+ if permillion and normvalue == 1.0: -+ assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data" -+ normvalue = float(data.mapped_reads)/1000000.0 - if current_chromosome and data.chromosome != current_chromosome or not lines: - for strand in strands: - if min_cov: -@@ -118,6 +117,8 @@ - if data.substitutions: chromdict[data.strand][data.substitutions] += data.number_of_reads - elif type == "deletions": - if data.deletions: chromdict[data.strand][data.deletions] += data.number_of_reads -+ else: -+ break - - def gtf2dropoffrates(gtffile,chromosomedata,out_files=[],score=False,log=sys.stdout,zeros=False,min_cov=0): - """Produces an sgr output file for hits, substitutions and deletions. It requires, besides data a file containing diff --git a/academic/pyCRAC/README b/academic/pyCRAC/README index dd847d0935..a5be782d73 100644 --- a/academic/pyCRAC/README +++ b/academic/pyCRAC/README @@ -1,8 +1,8 @@ The pyCRAC package is a collection of python2-scripts to analyse high -throughput data generated by RNA-sequencing, especially of molecules -crosslinked by UV to an immunoprecipitated protein of interest (i.e. -data generated by CLIP or CRAC protocols). -It can be used to remove duplicate reads,tackles directional libraries +throughput data generated by RNA-sequencing, especially of molecules +crosslinked by UV to an immunoprecipitated protein of interest (i.e. +data generated by CLIP or CRAC protocols). +It can be used to remove duplicate reads,tackles directional libraries and reports sense and anti-sense hits. Included is the pipeline used for the analysis of a group of CRAC data diff --git a/academic/pyCRAC/pyCRAC.SlackBuild b/academic/pyCRAC/pyCRAC.SlackBuild index 7a386f452d..89f9a3fd65 100644 --- a/academic/pyCRAC/pyCRAC.SlackBuild +++ b/academic/pyCRAC/pyCRAC.SlackBuild @@ -23,12 +23,12 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=pyCRAC -VERSION=${VERSION:-1.2.3.0} +VERSION=${VERSION:-1.2.4.0} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} SRCNAM=sgrann-pycrac -SRCVER=${SRCVER:-8792459eeef7} +SRCVER=${SRCVER:-eadda2b95c34} PIPENAM=kinetic_crac_pipeline PIPEVER=${PIPEVER:-73dff1be9488} @@ -73,8 +73,6 @@ mkdir $PRGNAM/$PIPENAM tar xvf $CWD/sgrann-$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 || \ tar xvf $CWD/$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 -patch -p1 < $CWD/GTF2-scripts.patch - #replace setup.py rm setup.py cp $CWD/setup_slack.py setup.py @@ -94,7 +92,7 @@ python setup.py install --root=$PKG find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true -# The pipeline-R script +# The pipeline-R script mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM cp $PRGNAM/$PIPENAM/gaussianProcessAnalysis.R $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM diff --git a/academic/pyCRAC/pyCRAC.info b/academic/pyCRAC/pyCRAC.info index 9051b43654..30f4980f21 100644 --- a/academic/pyCRAC/pyCRAC.info +++ b/academic/pyCRAC/pyCRAC.info @@ -1,9 +1,9 @@ PRGNAM="pyCRAC" -VERSION="1.2.3.0" +VERSION="1.2.4.0" HOMEPAGE="https://bitbucket.org/sgrann/" -DOWNLOAD="https://bitbucket.org/sgrann/pycrac/get/8792459eeef7.tar.gz \ +DOWNLOAD="https://bitbucket.org/sgrann/pycrac/get/eadda2b95c34.tar.gz \ https://bitbucket.org/sgrann/kinetic_crac_pipeline/get/73dff1be9488.tar.gz" -MD5SUM="a0e05b812dc765a2b1f673078ea43e3d \ +MD5SUM="c6b37913a6f7da123e3243166806aa56 \ 8f968d1dca38aa2b3ac401ba8da70cef" DOWNLOAD_x86_64="" MD5SUM_x86_64="" diff --git a/academic/pyCRAC/setup_slack.py b/academic/pyCRAC/setup_slack.py index 621b944573..334e9c6a82 100644 --- a/academic/pyCRAC/setup_slack.py +++ b/academic/pyCRAC/setup_slack.py @@ -2,7 +2,7 @@ # not compatible with python 3 __author__ = "Sander Granneman" __copyright__ = "Copyright 2017" -__version__ = "1.2.3.0" +__version__ = "1.2.4.0" __credits__ = ["Sander Granneman","Hywell Dunn Davies"] __maintainer__ = ["Rob van Nues, via SlackBuilds.org"] __email__ = "sgrannem@staffmail.ed.ac.uk" |