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academic/pyCRAC: Updated for version 1.2.4.0.
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
This commit is contained in:
rob van nues
Willy Sudiarto Raharjo
parent
cca112722f
commit
da57b65b95
5 changed files with 11 additions and 92 deletions
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@ -1,79 +0,0 @@
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diff -Naur sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2bedGraph.py sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2bedGraph.py
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--- sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2bedGraph.py 2017-09-11 15:11:12.000000000 +0100
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+++ sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2bedGraph.py 2017-09-10 00:47:13.014633000 +0100
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@@ -2,7 +2,7 @@
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# not compatible with python 3
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__author__ = "Sander Granneman"
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__copyright__ = "Copyright 2017"
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-__version__ = "0.0.7"
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+__version__ = "0.0.6"
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__credits__ = ["Sander Granneman"]
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__maintainer__ = "Sander Granneman"
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__email__ = "sgrannem@staffmail.ed.ac.uk"
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@@ -80,14 +80,12 @@
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chromdata = processChromFile(chromlengthfile)
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###
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- normvalue = 1.0
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- if permillion and normvalue == 1.0:
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- assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
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- normvalue = float(data.mapped_reads)/1000000.0
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-
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while True:
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lines = data.readLineByLine()
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- # to normalize the data to per million reads
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+ normvalue = 1.0
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+ if permillion and normvalue == 1.0:
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+ assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
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+ normvalue = float(data.mapped_reads)/1000000.0 # to normalize the data to per million reads
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if current_chromosome and data.chromosome != current_chromosome or not lines:
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for strand in chromdict:
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start = 0
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diff -Naur sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2sgr.py sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2sgr.py
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--- sgrann-pycrac-8792459eeef7/pyCRAC/scripts/pyGTF2sgr.py 2017-09-11 15:11:12.000000000 +0100
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+++ sgrann-pycrac-8792459eeef7-slack/pyCRAC/scripts/pyGTF2sgr.py 2017-09-10 00:47:13.014633000 +0100
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@@ -1,8 +1,8 @@
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#!/usr/bin/python
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# not compatible with python 3
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__author__ = "Sander Granneman"
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-__copyright__ = "Copyright 2017"
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-__version__ = "0.0.6"
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+__copyright__ = "Copyright 2015"
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+__version__ = "0.0.5"
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__credits__ = ["Sander Granneman"]
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__maintainer__ = "Sander Granneman"
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__email__ = "sgrannem@staffmail.ed.ac.uk"
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@@ -13,7 +13,7 @@
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# pyGTF2sgr.py
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#
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#
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-# Copyright (c) Sander Granneman 2017
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+# Copyright (c) Sander Granneman 2015
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal
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@@ -73,12 +73,11 @@
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###
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normvalue = 1.0
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- if permillion:
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- assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
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- normvalue = float(data.mapped_reads)/1000000.0
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-
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while True:
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lines = data.readLineByLine()
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+ if permillion and normvalue == 1.0:
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+ assert data.mapped_reads, "No information on the number of mapped reads could be found in the gtf file. Cannot normalize the data"
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+ normvalue = float(data.mapped_reads)/1000000.0
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if current_chromosome and data.chromosome != current_chromosome or not lines:
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for strand in strands:
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if min_cov:
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@@ -118,6 +117,8 @@
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if data.substitutions: chromdict[data.strand][data.substitutions] += data.number_of_reads
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elif type == "deletions":
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if data.deletions: chromdict[data.strand][data.deletions] += data.number_of_reads
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+ else:
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+ break
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def gtf2dropoffrates(gtffile,chromosomedata,out_files=[],score=False,log=sys.stdout,zeros=False,min_cov=0):
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"""Produces an sgr output file for hits, substitutions and deletions. It requires, besides data a file containing
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@ -1,8 +1,8 @@
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The pyCRAC package is a collection of python2-scripts to analyse high
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throughput data generated by RNA-sequencing, especially of molecules
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crosslinked by UV to an immunoprecipitated protein of interest (i.e.
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data generated by CLIP or CRAC protocols).
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It can be used to remove duplicate reads,tackles directional libraries
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throughput data generated by RNA-sequencing, especially of molecules
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crosslinked by UV to an immunoprecipitated protein of interest (i.e.
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data generated by CLIP or CRAC protocols).
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It can be used to remove duplicate reads,tackles directional libraries
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and reports sense and anti-sense hits.
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Included is the pipeline used for the analysis of a group of CRAC data
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@ -23,12 +23,12 @@
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# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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PRGNAM=pyCRAC
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VERSION=${VERSION:-1.2.3.0}
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VERSION=${VERSION:-1.2.4.0}
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BUILD=${BUILD:-1}
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TAG=${TAG:-_SBo}
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SRCNAM=sgrann-pycrac
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SRCVER=${SRCVER:-8792459eeef7}
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SRCVER=${SRCVER:-eadda2b95c34}
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PIPENAM=kinetic_crac_pipeline
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PIPEVER=${PIPEVER:-73dff1be9488}
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@ -73,8 +73,6 @@ mkdir $PRGNAM/$PIPENAM
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tar xvf $CWD/sgrann-$PIPENAM-$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1 || \
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tar xvf $CWD/$PIPEVER.tar.gz -C $PRGNAM/$PIPENAM --strip-components=1
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patch -p1 < $CWD/GTF2-scripts.patch
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#replace setup.py
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rm setup.py
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cp $CWD/setup_slack.py setup.py
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@ -94,7 +92,7 @@ python setup.py install --root=$PKG
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find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
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| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
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# The pipeline-R script
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# The pipeline-R script
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mkdir -p $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM
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cp $PRGNAM/$PIPENAM/gaussianProcessAnalysis.R $PKG/usr/share/$PRGNAM-$VERSION/$PIPENAM
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@ -1,9 +1,9 @@
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PRGNAM="pyCRAC"
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VERSION="1.2.3.0"
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VERSION="1.2.4.0"
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HOMEPAGE="https://bitbucket.org/sgrann/"
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DOWNLOAD="https://bitbucket.org/sgrann/pycrac/get/8792459eeef7.tar.gz \
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DOWNLOAD="https://bitbucket.org/sgrann/pycrac/get/eadda2b95c34.tar.gz \
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https://bitbucket.org/sgrann/kinetic_crac_pipeline/get/73dff1be9488.tar.gz"
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MD5SUM="a0e05b812dc765a2b1f673078ea43e3d \
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MD5SUM="c6b37913a6f7da123e3243166806aa56 \
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8f968d1dca38aa2b3ac401ba8da70cef"
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DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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@ -2,7 +2,7 @@
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# not compatible with python 3
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__author__ = "Sander Granneman"
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__copyright__ = "Copyright 2017"
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__version__ = "1.2.3.0"
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__version__ = "1.2.4.0"
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__credits__ = ["Sander Granneman","Hywell Dunn Davies"]
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__maintainer__ = ["Rob van Nues, via SlackBuilds.org"]
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__email__ = "sgrannem@staffmail.ed.ac.uk"
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