| Previous changeset 8:82bb8c455761 (2016-03-30) Next changeset 10:96bf4ee28e57 (2016-03-30) |
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Commit message:
Uploaded |
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modified:
ezBAMQC/Makefile ezBAMQC/README.rst ezBAMQC/ezBAMQC ezBAMQC/setup.py |
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added:
._ezBAMQC ezBAMQC/._MANIFEST.in ezBAMQC/._Makefile ezBAMQC/._README.rst ezBAMQC/._doc ezBAMQC/._ezBAMQC ezBAMQC/._setup.py ezBAMQC/._src ezBAMQC/._test-data ezBAMQC/doc/._CONTACTS ezBAMQC/doc/._COPYING ezBAMQC/doc/._INSTALL ezBAMQC/doc/._THANKS ezBAMQC/doc/._bamqc-icon.gif ezBAMQC/doc/._bamqc-icon.png ezBAMQC/doc/bamqc-icon.gif ezBAMQC/src/._ezBAMQC ezBAMQC/src/._htslib ezBAMQC/src/ezBAMQC/._Constants.h ezBAMQC/src/ezBAMQC/._Coverage_prof.cpp ezBAMQC/src/ezBAMQC/._Coverage_prof.h ezBAMQC/src/ezBAMQC/._GeneFeatures.cpp ezBAMQC/src/ezBAMQC/._GeneFeatures.h ezBAMQC/src/ezBAMQC/._InnerDist_prof.cpp ezBAMQC/src/ezBAMQC/._InnerDist_prof.h ezBAMQC/src/ezBAMQC/._IntervalTree.cpp ezBAMQC/src/ezBAMQC/._IntervalTree.h ezBAMQC/src/ezBAMQC/._Mappability.cpp ezBAMQC/src/ezBAMQC/._Mappability.h ezBAMQC/src/ezBAMQC/._ReadDup_prof.cpp ezBAMQC/src/ezBAMQC/._ReadDup_prof.h ezBAMQC/src/ezBAMQC/._Results.cpp ezBAMQC/src/ezBAMQC/._Results.h ezBAMQC/src/ezBAMQC/._parseBAM.cpp ezBAMQC/src/ezBAMQC/._parseBAM.h ezBAMQC/src/ezBAMQC/._rRNA.cpp ezBAMQC/src/ezBAMQC/._rRNA.h ezBAMQC/src/ezBAMQC/._sam.h ezBAMQC/src/htslib/._INSTALL ezBAMQC/src/htslib/._LICENSE ezBAMQC/src/htslib/._Makefile ezBAMQC/src/htslib/._NEWS ezBAMQC/src/htslib/._README ezBAMQC/src/htslib/._bgzf.c ezBAMQC/src/htslib/._bgzip.c ezBAMQC/src/htslib/._config.h ezBAMQC/src/htslib/._config.mk ezBAMQC/src/htslib/._config.mk.in ezBAMQC/src/htslib/._configure ezBAMQC/src/htslib/._configure.ac ezBAMQC/src/htslib/._cram ezBAMQC/src/htslib/._faidx.5 ezBAMQC/src/htslib/._faidx.c ezBAMQC/src/htslib/._hfile.c ezBAMQC/src/htslib/._hfile_internal.h ezBAMQC/src/htslib/._hfile_irods.c ezBAMQC/src/htslib/._hfile_net.c ezBAMQC/src/htslib/._hts.c ezBAMQC/src/htslib/._htsfile.1 ezBAMQC/src/htslib/._htsfile.c ezBAMQC/src/htslib/._htslib ezBAMQC/src/htslib/._htslib.mk ezBAMQC/src/htslib/._htslib.pc.in ezBAMQC/src/htslib/._htslib_vars.mk ezBAMQC/src/htslib/._kfunc.c ezBAMQC/src/htslib/._knetfile.c ezBAMQC/src/htslib/._kstring.c ezBAMQC/src/htslib/._regidx.c ezBAMQC/src/htslib/._sam.5 ezBAMQC/src/htslib/._sam.c ezBAMQC/src/htslib/._synced_bcf_reader.c ezBAMQC/src/htslib/._tabix.1 ezBAMQC/src/htslib/._tabix.c ezBAMQC/src/htslib/._tbx.c ezBAMQC/src/htslib/._test ezBAMQC/src/htslib/._vcf.5 ezBAMQC/src/htslib/._vcf.c ezBAMQC/src/htslib/._vcf_sweep.c ezBAMQC/src/htslib/._vcfutils.c ezBAMQC/src/htslib/._version.h ezBAMQC/src/htslib/cram/._cram.h ezBAMQC/src/htslib/cram/._cram_codecs.c ezBAMQC/src/htslib/cram/._cram_codecs.h ezBAMQC/src/htslib/cram/._cram_decode.c ezBAMQC/src/htslib/cram/._cram_decode.h ezBAMQC/src/htslib/cram/._cram_encode.c ezBAMQC/src/htslib/cram/._cram_encode.h ezBAMQC/src/htslib/cram/._cram_index.c ezBAMQC/src/htslib/cram/._cram_index.h ezBAMQC/src/htslib/cram/._cram_io.c ezBAMQC/src/htslib/cram/._cram_io.h ezBAMQC/src/htslib/cram/._cram_samtools.c ezBAMQC/src/htslib/cram/._cram_samtools.h ezBAMQC/src/htslib/cram/._cram_stats.c ezBAMQC/src/htslib/cram/._cram_stats.h ezBAMQC/src/htslib/cram/._cram_structs.h ezBAMQC/src/htslib/cram/._files.c ezBAMQC/src/htslib/cram/._mFILE.c ezBAMQC/src/htslib/cram/._mFILE.h ezBAMQC/src/htslib/cram/._md5.c ezBAMQC/src/htslib/cram/._md5.h ezBAMQC/src/htslib/cram/._misc.h ezBAMQC/src/htslib/cram/._open_trace_file.c ezBAMQC/src/htslib/cram/._open_trace_file.h ezBAMQC/src/htslib/cram/._os.h ezBAMQC/src/htslib/cram/._pooled_alloc.c ezBAMQC/src/htslib/cram/._pooled_alloc.h ezBAMQC/src/htslib/cram/._rANS_byte.h ezBAMQC/src/htslib/cram/._rANS_static.c ezBAMQC/src/htslib/cram/._rANS_static.h ezBAMQC/src/htslib/cram/._sam_header.c ezBAMQC/src/htslib/cram/._sam_header.h ezBAMQC/src/htslib/cram/._string_alloc.c ezBAMQC/src/htslib/cram/._string_alloc.h ezBAMQC/src/htslib/cram/._thread_pool.c ezBAMQC/src/htslib/cram/._thread_pool.h ezBAMQC/src/htslib/cram/._vlen.c ezBAMQC/src/htslib/cram/._vlen.h ezBAMQC/src/htslib/cram/._zfio.c ezBAMQC/src/htslib/cram/._zfio.h ezBAMQC/src/htslib/htslib/._bgzf.h ezBAMQC/src/htslib/htslib/._faidx.h ezBAMQC/src/htslib/htslib/._hfile.h ezBAMQC/src/htslib/htslib/._hts.h ezBAMQC/src/htslib/htslib/._hts_defs.h ezBAMQC/src/htslib/htslib/._kfunc.h ezBAMQC/src/htslib/htslib/._khash.h ezBAMQC/src/htslib/htslib/._khash_str2int.h ezBAMQC/src/htslib/htslib/._klist.h ezBAMQC/src/htslib/htslib/._knetfile.h ezBAMQC/src/htslib/htslib/._kseq.h ezBAMQC/src/htslib/htslib/._ksort.h ezBAMQC/src/htslib/htslib/._kstring.h ezBAMQC/src/htslib/htslib/._regidx.h ezBAMQC/src/htslib/htslib/._sam.h ezBAMQC/src/htslib/htslib/._synced_bcf_reader.h ezBAMQC/src/htslib/htslib/._tbx.h ezBAMQC/src/htslib/htslib/._vcf.h ezBAMQC/src/htslib/htslib/._vcf_sweep.h ezBAMQC/src/htslib/htslib/._vcfutils.h ezBAMQC/src/htslib/test/._auxf#values.sam ezBAMQC/src/htslib/test/._auxf.fa ezBAMQC/src/htslib/test/._auxf.fa.fai ezBAMQC/src/htslib/test/._c1#bounds.sam ezBAMQC/src/htslib/test/._c1#clip.sam ezBAMQC/src/htslib/test/._c1#pad1.sam ezBAMQC/src/htslib/test/._c1#pad2.sam ezBAMQC/src/htslib/test/._c1#pad3.sam ezBAMQC/src/htslib/test/._c1.fa ezBAMQC/src/htslib/test/._c1.fa.fai ezBAMQC/src/htslib/test/._ce#1.sam ezBAMQC/src/htslib/test/._ce#2.sam ezBAMQC/src/htslib/test/._ce#5.sam ezBAMQC/src/htslib/test/._ce#5b.sam ezBAMQC/src/htslib/test/._ce#large_seq.sam ezBAMQC/src/htslib/test/._ce#tag_depadded.sam ezBAMQC/src/htslib/test/._ce#tag_padded.sam ezBAMQC/src/htslib/test/._ce#unmap.sam ezBAMQC/src/htslib/test/._ce#unmap1.sam ezBAMQC/src/htslib/test/._ce#unmap2.sam ezBAMQC/src/htslib/test/._ce.fa ezBAMQC/src/htslib/test/._ce.fa.fai ezBAMQC/src/htslib/test/._compare_sam.pl ezBAMQC/src/htslib/test/._fieldarith.c ezBAMQC/src/htslib/test/._fieldarith.sam ezBAMQC/src/htslib/test/._hfile.c ezBAMQC/src/htslib/test/._sam.c ezBAMQC/src/htslib/test/._test-regidx.c ezBAMQC/src/htslib/test/._test-vcf-api.c ezBAMQC/src/htslib/test/._test-vcf-api.out ezBAMQC/src/htslib/test/._test-vcf-sweep.c ezBAMQC/src/htslib/test/._test-vcf-sweep.out ezBAMQC/src/htslib/test/._test.pl ezBAMQC/src/htslib/test/._test_view.c ezBAMQC/src/htslib/test/._test_view.pl ezBAMQC/src/htslib/test/._xx#blank.sam ezBAMQC/src/htslib/test/._xx#large_aux.sam ezBAMQC/src/htslib/test/._xx#large_aux2.sam ezBAMQC/src/htslib/test/._xx#minimal.sam ezBAMQC/src/htslib/test/._xx#pair.sam ezBAMQC/src/htslib/test/._xx#rg.sam ezBAMQC/src/htslib/test/._xx#triplet.sam ezBAMQC/src/htslib/test/._xx#unsorted.sam ezBAMQC/src/htslib/test/._xx.fa ezBAMQC/src/htslib/test/._xx.fa.fai ezBAMQC/test-data/._exp_data ezBAMQC/test-data/._output ezBAMQC/test-data/exp_data/._hg19_rRNA.bed ezBAMQC/test-data/exp_data/._hg19_refGene.gtf.tar.gz ezBAMQC/test-data/exp_data/._treat1.bam ezBAMQC/test-data/exp_data/._treat2.bam ezBAMQC/test-data/exp_data/._treat3.bam ezBAMQC/test-data/output/._data ezBAMQC/test-data/output/._ezBAMQC_output.html ezBAMQC/test-data/output/._figs ezBAMQC/test-data/output/data/._smp0.ReadLen_plot.r ezBAMQC/test-data/output/data/._smp0.TransCoverage.r ezBAMQC/test-data/output/data/._smp0.clipping_profile.r ezBAMQC/test-data/output/data/._smp0.clipping_profile.xls ezBAMQC/test-data/output/data/._smp0.geneAbundance.txt ezBAMQC/test-data/output/data/._smp0.geneBodyCoverage.txt ezBAMQC/test-data/output/data/._smp0.geneBodyCoverage_plot.r ezBAMQC/test-data/output/data/._smp0.mapq_profile.r ezBAMQC/test-data/output/data/._smp0.mapq_profile.xls ezBAMQC/test-data/output/data/._smp0.read_distr.r ezBAMQC/test-data/output/data/._smp0.read_distr_pie.r ezBAMQC/test-data/output/data/._smp0.readlen_profile.xls ezBAMQC/test-data/output/data/._smp0.res.txt ezBAMQC/test-data/output/data/._smp1.ReadLen_plot.r ezBAMQC/test-data/output/data/._smp1.TransCoverage.r ezBAMQC/test-data/output/data/._smp1.clipping_profile.r ezBAMQC/test-data/output/data/._smp1.clipping_profile.xls ezBAMQC/test-data/output/data/._smp1.geneAbundance.txt ezBAMQC/test-data/output/data/._smp1.geneBodyCoverage.txt ezBAMQC/test-data/output/data/._smp1.geneBodyCoverage_plot.r ezBAMQC/test-data/output/data/._smp1.mapq_profile.r ezBAMQC/test-data/output/data/._smp1.mapq_profile.xls ezBAMQC/test-data/output/data/._smp1.read_distr.r ezBAMQC/test-data/output/data/._smp1.read_distr_pie.r ezBAMQC/test-data/output/data/._smp1.readlen_profile.xls ezBAMQC/test-data/output/data/._smp1.res.txt ezBAMQC/test-data/output/data/._smp2.ReadLen_plot.r ezBAMQC/test-data/output/data/._smp2.TransCoverage.r ezBAMQC/test-data/output/data/._smp2.clipping_profile.r ezBAMQC/test-data/output/data/._smp2.clipping_profile.xls ezBAMQC/test-data/output/data/._smp2.geneAbundance.txt ezBAMQC/test-data/output/data/._smp2.geneBodyCoverage.txt ezBAMQC/test-data/output/data/._smp2.geneBodyCoverage_plot.r ezBAMQC/test-data/output/data/._smp2.mapq_profile.r ezBAMQC/test-data/output/data/._smp2.mapq_profile.xls ezBAMQC/test-data/output/data/._smp2.read_distr.r ezBAMQC/test-data/output/data/._smp2.read_distr_pie.r ezBAMQC/test-data/output/data/._smp2.readlen_profile.xls ezBAMQC/test-data/output/data/._smp2.res.txt ezBAMQC/test-data/output/data/._smp_correlation.r ezBAMQC/test-data/output/figs/._smp0.TransCoverage.png ezBAMQC/test-data/output/figs/._smp0.clipping_profile.png ezBAMQC/test-data/output/figs/._smp0.geneBodyCoverage.png ezBAMQC/test-data/output/figs/._smp0.mapq_profile.png ezBAMQC/test-data/output/figs/._smp0.read_distr.png ezBAMQC/test-data/output/figs/._smp0.read_distr_pie.png ezBAMQC/test-data/output/figs/._smp0.readlen_profile.png ezBAMQC/test-data/output/figs/._smp1.TransCoverage.png ezBAMQC/test-data/output/figs/._smp1.clipping_profile.png ezBAMQC/test-data/output/figs/._smp1.geneBodyCoverage.png ezBAMQC/test-data/output/figs/._smp1.mapq_profile.png ezBAMQC/test-data/output/figs/._smp1.read_distr.png ezBAMQC/test-data/output/figs/._smp1.read_distr_pie.png ezBAMQC/test-data/output/figs/._smp1.readlen_profile.png ezBAMQC/test-data/output/figs/._smp2.TransCoverage.png ezBAMQC/test-data/output/figs/._smp2.clipping_profile.png ezBAMQC/test-data/output/figs/._smp2.geneBodyCoverage.png ezBAMQC/test-data/output/figs/._smp2.mapq_profile.png ezBAMQC/test-data/output/figs/._smp2.read_distr.png ezBAMQC/test-data/output/figs/._smp2.read_distr_pie.png ezBAMQC/test-data/output/figs/._smp2.readlen_profile.png ezBAMQC/test-data/output/figs/._smp_corr.png ezBAMQC/test-data/output/figs/._smp_cov.png ezBAMQC/test-data/output/figs/._smp_qual.png ezBAMQC/test-data/output/figs/._smp_reproducibility.png ezBAMQC/test-data/output/figs/._smp_var.png |
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removed:
BAMqc.sh BAMqc.xml cshl_geneGTF.loc.sample cshl_rRNA_BED.loc.sample ezBAMQC.zip tool_data_table_conf.xml.sample |
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| diff -r 82bb8c455761 -r 6610eedd9fae ._ezBAMQC |
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| Binary file ._ezBAMQC has changed |
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| diff -r 82bb8c455761 -r 6610eedd9fae BAMqc.sh --- a/BAMqc.sh Wed Mar 30 12:03:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,122 +0,0 @@ -#!/bin/sh - -### Galaxy Wrapper for BAMqc ### - -alignment_files="" -refgene="" -attrID="" -rRNA="" -outputHTML="" -stranded="" -mapq="30" -lowBound="-250" -upperBound="250" -stepSize="5" -labels="" -cores="1" - -ARGS=$(getopt -o "r:f:R:o:s:p:q:" -- "$@") - -if [ $? -ne 0 ]; then - echo "Invalid command-line parameters. Do not use this script outside of Galaxy" >&2 - exit 1 -fi - -eval set -- "$ARGS" - -while [ $# -gt 0 ]; do - case "$1" in - -r) - refgene="$2" - shift 2 - ;; - -f) - attrID="$2" - shift 2 - ;; - -R) - rRNA="$2" - shift 2 - ;; - -o) - outputHTML=$2 - shift 2 - ;; - -s) - stranded=$2 - shift 2 - ;; - -q) - mapq=$2 - shift 2 - ;; - - -p) - cores=$2 - shift 2 - ;; - --) - shift - break - ;; - esac -done - -if [ "$cores" -gt 10 ];then - cores="10" -fi - -outputDir=`echo $outputHTML | sed 's/\.dat$/_files/'` -if [ ! -d "$outputDir" ]; then - mkdir $outputDir -fi - -touch bamqc.log - -while [ "$#" -ne 0 ]; -do - FILE="$1" - LABEL=`echo $2 | sed 's/ /-/g; s/\[//; s/\]//;'` - shift 2 - QNAME_SORTED=`samtools view -H ${FILE} | grep "SO:queryname"` - if [ $? -ne 0 ]; then - BASE=`basename ${FILE} \.dat` - echo "Sorting BAM file (${LABEL}." >>samtools.log - samtools sort -@ 5 -n ${FILE} ${BASE} 2>>samtools.log - if [ $? -ne 0 ]; then - echo "Error with samtools sorting for BAM file (${LABEL})." >&2 - cat samtools.log >&2 - exit 1 - fi - echo "BAM file (${LABEL}) was re-sorted by query name." >>bamqc.log - FILELIST="$FILELIST ${BASE}.bam" - else - FILELIST="$FILELIST $FILE" - fi - LABELLIST="$LABELLIST $LABEL" -done - -CMD="ezBAMQC -i $FILELIST -l $LABELLIST -f $attrID -r $refgene -o Galaxy_BAMqc_output --stranded $stranded -q $mapq --rRNA $rRNA -t $cores" - -echo "BAMqc command: $CMD" >> bamqc.log -echo >> bamqc.log - -$CMD 2>> bamqc.log - -if [ $? -ne 0 ]; then - echo "BAMqc ran with errors" >&2 - cat bamqc.log >&2 - exit 1 -fi - -sed -i "s/\.\.\/Galaxy_BAMqc_output\///g;" Galaxy_BAMqc_output/bamqc_output.html - -cp -r Galaxy_BAMqc_output/data "$outputDir" -cp -r Galaxy_BAMqc_output/figs "$outputDir" -cp Galaxy_BAMqc_output/bamqc_output.html "$outputHTML" - -if [ $? -ne 0 ]; then - echo "Copying BAMqc results failed" >&2 -fi - -echo "BAMqc results copied to $outputDir" >>bamqc.log |
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| diff -r 82bb8c455761 -r 6610eedd9fae BAMqc.xml --- a/BAMqc.xml Wed Mar 30 12:03:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,109 +0,0 @@ -<tool id="cshl_BAMqc" name="ezBAMQC" version="0.6.7" > - - <description> - performs QC on BAM files for gene abundances and sample correlation - </description> - - <requirements> - <requirement type="package">BAMqc</requirement> - <requirement type="package">samtools</requirement> - <requirement type="package">R</requirement> - </requirements> - - <command interpreter="sh"> - - BAMqc.sh - - -r '${refdb}' - - -f '${attrID}' - - -R '${rRNAdb}' - - -s '$stranded' - - -o "$output" - - #set $core = len($files) - - -p $core - - #if str($cond_adv_options.adv_options) == 'yes': - -q '$cond_adv_options.mapq' - #end if - - #for $file in $files - '$file.input' - '$file.input.tag' - #end for - - </command> - - <inputs> - <repeat name="files" title="BAM files" min="1"> - <param format="bam" name="input" type="data" label="Files for QC" /> - </repeat> - - <param name="refdb" type="select" label="Reference gene model (GTF)"> - <options from_data_table="gene_GTF_database" /> - </param> - - <param name="attrID" type="text" size="50" value="gene_id" label="Feature ID name" help="Summing reads based on gene (gene_id) or transcript (transcript_id."> - <sanitizer> - <valid initial="none"> - <add value="ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz01234567890_-." /> - </valid> - </sanitizer> - </param> - - <param name="rRNAdb" type="select" label="Ribosomal RNA locations (BED)"> - <options from_data_table="rRNA_BED_database" /> - </param> - - <param name="stranded" type="select" label="Strandedness"> - <option value="yes">Yes - Read from stranded library</option> - <option value="no">No - Reads from unstranded library</option> - <option value="reverse">Reverse - reverse-stranded library (e.g. NSR)</option> - </param> - - <conditional name="cond_adv_options"> - <param name="adv_options" type="select" label="Set advanced options"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - - <when value="yes"> - <param name="mapq" type="integer" value="30" label="Minimum mapping quality for an alignment to be called uniquely mapped" /> - </when> - - <when value="no" /> - </conditional> - - </inputs> - - <outputs> - <data format="html" name="output" label="BAM QC on $on_tag_string" /> - <data format="txt" name="log" from_work_dir="bamqc.log" label="ezBAMQC log output" hidden="True" /> - </outputs> - - <help> - -**What it does** - -This tool takes the mapping results from RNA-Seq libraries (BAM), and performs rapid gene abundance quantification. If multiple files are provided, it will calculate and display correlation between each sample. - ------ - -The Galaxy wrapper for this tool is written by the `Cold Spring Harbor Laboratory`_ `Bioinformatics Shared Resources`_. - -ezBAMQC_ is written by the `Molly Hammell Laboratory`_ and the `Bioinformatics Shared Resources`_ at CSHL_. - -.. _CSHL: `Cold Spring Harbor Laboratory`_ -.. _ezBAMQC: http://hammelllab.labsites.cshl.edu/software#ezBAMQC -.. _`Molly Hammell Laboratory`: http://hammelllab.labsites.cshl.edu/ -.. _`Cold Spring Harbor Laboratory`: http://www.cshl.edu/ -.. _`Bioinformatics Shared Resources`: http://bioinfo.cshl.edu/index.html - - </help> -</tool> - |
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| diff -r 82bb8c455761 -r 6610eedd9fae cshl_geneGTF.loc.sample --- a/cshl_geneGTF.loc.sample Wed Mar 30 12:03:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,20 +0,0 @@ -## -## Location of gene annotations GTF -## -## Format is: -## value<TAB>Name<TAB>dbkey<TAB>ID -## -## Name can contain spaces - -/localdata1/annotations/GTF/latest/hg19_refGene.gtf hg19 UCSC refSeq hg19 hg19_refgene -/localdata1/annotations/GTF/latest/hg18_refGene.gtf hg18 UCSC refSeq hg18 hg18_refgene -/localdata1/annotations/GTF/latest/mm10_refGene.gtf mm10 UCSC refSeq mm10 mm10_refgene -/localdata1/annotations/GTF/latest/mm9_refGene.gtf mm9 UCSC refSeq mm9 mm9_refgene -/localdata1/annotations/GTF/latest/dm3_refGene.gtf dm3 UCSC refSeq dm3 dm3_refgene -/localdata1/annotations/GTF/refseq_2015_01_20/rn5_refGene.gtf rn5 UCSC refSeq rn5 rn5_refgene -#/localdata1/annotations/GTF/latest/rn4_refGene.gtf rn4 UCSC refSeq rn4 rn4_refgene -#/localdata1/annotations/GTF/latest/ce6_refGene.gtf ce6 UCSC refSeq ce6 ce6_refgene -#/localdata1/annotations/GTF/latest/ce10_refGene.gtf ce10 UCSC refSeq ce10 ce10_refgene -#/localdata1/annotations/GTF/igenomes_2014_08_28/ZmAGPv2_iGenome_genes.gtf Maize (AGPv2) iGenomes gene info ZmAGPv2 ZmAGPv2_genes -#/localdata1/annotations/GTF/igenomes_2014_08_28/ZmAGPv3_iGenome_genes.gtf Maize (AGPv3) iGenomes gene info ZmAGPv3 ZmAGPv3_genes -#/localdata1/annotations/GTF/igenomes_2014_08_28/tair10_iGenome_genes.gtf Arabidopsis (TAIR10) iGenomes gene info |
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| @@ -1,19 +0,0 @@ -## -## Location of rRNA BED files -## -## Format is: -## value<TAB>Name<TAB>dbkey<TAB>ID -## -## Name can contain spaces - -#/localdata1/annotations/BED_files/rRNA/hg19_rmsk_rRNA.bed hg38 repeatMasker rRNA hg38 hg38_rRNA -/localdata1/annotations/BED_files/rRNA/hg19_rmsk_rRNA.bed hg19 repeatMasker rRNA hg19 hg19_rRNA -/localdata1/annotations/BED_files/rRNA/hg18_rmsk_rRNA.bed hg18 repeatMasker rRNA hg18 hg18_rRNA -/localdata1/annotations/BED_files/rRNA/mm10_rmsk_rRNA.bed mm10 repeatMasker rRNA mm10 mm10_rRNA -/localdata1/annotations/BED_files/rRNA/mm9_rmsk_rRNA.bed mm9 repeatMasker rRNA mm9 mm9_rRNA -#/localdata1/annotations/BED_files/rRNA/dm6_rmsk_rRNA.bed dm6 repeatMasker rRNA dm6 dm6_rRNA -/localdata1/annotations/BED_files/rRNA/dm3_rmsk_rRNA.bed dm3 repeatMasker rRNA dm3 dm3_rRNA -/localdata1/annotations/BED_files/rRNA/rn5_rmsk_rRNA.bed rn5 repeatMasker rRNA rn5 rn5_rRNA -#/localdata1/annotations/BED_files/rRNA/rn4_rmsk_rRNA.bed rn4 repeatMasker rRNA rn4 rn4_rRNA -#/localdata1/annotations/BED_files/rRNA/ce6_rmsk_rRNA.bed ce6 repeatMasker rRNA ce6 ce6_rRNA -#/localdata1/annotations/BED_files/rRNA/ce10_rmsk_rRNA.bed ce10 repeatMasker rRNA ce10 ce10_rRNA \ No newline at end of file |
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| diff -r 82bb8c455761 -r 6610eedd9fae ezBAMQC/Makefile --- a/ezBAMQC/Makefile Wed Mar 30 12:03:10 2016 -0400 +++ b/ezBAMQC/Makefile Wed Mar 30 12:11:46 2016 -0400 |
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| @@ -1,6 +1,6 @@ # Makefile for ezBAMQC, utilities for the Sequence Alignment/Map format. # -# Version 0.6.5 +# Version 0.6.7 # # Copyright (C) 2015 Bioinformatics Shared Resource, CSHL. # Portions copyright (C) 2015 Cold Spring Harbor Laboratory. |
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| diff -r 82bb8c455761 -r 6610eedd9fae ezBAMQC/README.rst --- a/ezBAMQC/README.rst Wed Mar 30 12:03:10 2016 -0400 +++ b/ezBAMQC/README.rst Wed Mar 30 12:11:46 2016 -0400 |
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| b'@@ -1,184 +1,186 @@\n-.. image:: https://raw.githubusercontent.com/mhammell-laboratory/bamqc/master/doc/bamqc-icon.png\r\n- :width: 200 px\r\n- :alt: generated at codeology.braintreepayments.com/mhammell-laboratory/bamqc\r\n- :align: right\r\n- :target: http://codeology.braintreepayments.com/mhammell-laboratory/bamqc\r\n-\r\n-=====\r\n-ezBAMQC\r\n-=====\r\n-*"ezBAMQC, a tool to check the quality of mapped next generation sequencing files."*\r\n-\r\n-:Description:\r\n-\r\n- ezBAMQC is a tool to check the quality of either one or many mapped next-generation-sequencing datasets. It conducts comprehensive evaluations of aligned sequencing data from multiple aspects including: clipping profile, mapping quality distribution, mapped read length distribution, genomic/transcriptomic mapping distribution, inner distance distribution (for paired-end reads), ribosomal RNA contamination, transcript 5\xe2\x80\x99 and 3\xe2\x80\x99 end bias, transcription dropout rate, sample correlations, sample reproducibility, sample variations. It outputs a set of tables and plots and one HTML page that contains a summary of the results. Many metrics are designed for RNA-seq data specifically, but ezBAMQC can be applied to any mapped sequencing dataset such as RNA-seq, CLIP-seq, GRO-seq, ChIP-seq, DNA-seq and so on. ::\r\n-\r\n-:Links:\r\n-\r\n- `Github Page <https://github.com/mhammell-laboratory/bamqc>`_\r\n-\r\n- `Pypi Page <https://pypi.python.org/pypi/ezBAMQC>`_\r\n-\r\n- `MHammell Lab <http://hammelllab.labsites.cshl.edu/software>`_\r\n-\r\n-:Authors:\r\n- Ying Jin, David Molik, and Molly Hammell\r\n-\r\n-:Version: 0.6.5\r\n-\r\n-:Contact:\r\n- Ying Jin (yjin@cshl.edu)\r\n-\r\n-Installation guide for ezBAMQC for from source installs\r\n-=====================================================\r\n-\r\n-When installing ezBAMQC there are several options, but the main point is: since ezBAMQC uses C++ STD 11 you\'ll need a version of GCC that can support that, this useally means 4.8 or 4.9. beyond that, you\'ll need Python, R and Corrplot for interfacing with the C code.\r\n-\r\n-:Intallation:\r\n- `Source Code <https://github.com/mhammell-laboratory/ezBAMQC/releases>`_\r\n-\r\n- `Pypi <https://pypi.python.org/pypi?:action=display&name=ezBAMQC>`_\r\n-\r\n-:Prerequisites:\r\n- * `python2.7 <https://www.python.org/download/releases/2.7/>`_\r\n- * `R <https://www.r-project.org/>`_\r\n- * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_\r\n- * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_ GCC 4.9.1 or greater is recomended for PyPi install \r\n-\r\n-:Notes:\r\n- * While there are multiple methods of installing the prerequistes it may help to look at (if using a yum based linux distro):*\r\n- * `Devtoolset-3 <https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/3/html/User_Guide/sect-Red_Hat_Developer_Toolset-Install.html>`_ for GCC compilers\r\n- * `IUS <https://ius.io/>`_ for Python2.7\r\n- * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)\r\n- * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems\r\n-\r\n-Setup\r\n-=====\r\n-\r\n-1) Make sure that the GCC comiler is in your PATH:\r\n-\r\n-::\r\n-\r\n- export PATH=/path/to/gcc:$PATH\r\n-\r\n-2) Make sure that python2.7 is in your PYTHONPATH:\r\n-\r\n-::\r\n-\r\n- export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH\r\n-\r\n-3) There are three methods of installation of ezBAMQC, from source, from setup.py, and from pypi, once prequistes are setup. \r\n-\r\n-From Source\r\n-~~~~~~~~~~~\r\n-\r\n-1) Download source \r\n-\r\n-2) Unpack tarball and go to the directory of the package: \r\n-\r\n-::\r\n-\r\n- tar xvfz bamqc-0.6.6.tar.gz\r\n-\r\n- cd bamqc-0.6.6\r\n-\r\n-3) Run make:\r\n-\r\n-::\r\n-\r\n- make\r\n-\r\n-From Setup.py\r\n-~~~~~~~~~~~~~\r\n-\r\n-::\r\n-\r\n- python2.7 setup.py install \r\n-\r\n-From Pypi\r\n-~~~~~~~~~\r\n-\r\n-::\r\n-\r\n- pip2.7 install BAMqc\r\n-\r\n-Usage\r\n-=====\r\n-\r\n-::\r\n-\r\n- ezBAMQC [-h] -i alignment_files [alignment_files ...] -r [refgene]\r\n- [-f [attrID]] [--rRNA [rRNA]] -o [dir'..b'py\n+~~~~~~~~~~~~~\n+\n+::\n+\n+ python2.7 setup.py install \n+\n+From Pypi\n+~~~~~~~~~\n+\n+::\n+\n+ pip2.7 install BAMqc\n+\n+Usage\n+=====\n+\n+::\n+\n+ ezBAMQC [-h] -i alignment_files [alignment_files ...] -r [refgene]\n+ [-f [attrID]] [--rRNA [rRNA]] -o [dir] [--stranded [stranded]]\n+ [-q [mapq]] [-l labels [labels ...]] [-t NUMTHREADS]\n+\n+optional arguments:\n+\n+::\n+\n+ -h, --help show this help message and exit.\n+ -i, --inputFile alignment files. Could be multiple SAM/BAM files separated by space. Required.\n+ -r, --refgene gene annotation file in GTF format. Required\n+ -f the read summation at which feature level in the GTF file. DEFAULT: gene_id.\n+ --rRNA rRNA coordinates in BED format.\n+ -o, --outputDir output directory. Required.\n+ --stranded strandness of the library? \n+ yes : sense stranded\n+ reverse : reverse stranded\n+ no : not stranded\n+ DEFAULT: yes.\n+ -q, --mapq Minimum mapping quality (phred scaled) for an alignment to be called uniquely mapped. DEFAULT:30\n+ -l, --label Labels of input files. DEFAULT:smp1 smp2 ...\n+ -t, --threads Number of threads to use. DEFAULT:1\n+\n+Example: \n+\n+::\n+\n+ ezBAMQC -i test-data/exp_data/treat1.bam test-data/exp_data/treat2.bam test-data/exp_data/treat3.bam -r test-data/exp_data/hg9_refGene.gtf -q 30 --rRNA test-data/exp_data/hg19_rRNA.bed -o exp_output2\n+\n+ Please find the example output from folder test-data.\n+\n+FAQ\n+===\n+Q: Why use ezBAMQC?\n+\n+A: ezBAMQC is efficient and easy to use. With one command line, it reports a comprehensive evaluation of the data with a set of plots and tables.The ability to assess multiple samples together with high efficiency make it especially useful in cases where there are a large number of samples from the same condition, genotype, or treatment. ezBAMQC was written in C++ and supports multithreading. A mouse RNA-seq sample with 120M alignments can be done in 8 minutes with 5 threads.\n+\n+Q: Why the total number of reads reported by ezBAMQC does not match with samtools flagstat?\n+\n+A: The difference is because of non-uniquely mapped reads or multiply aligned reads (multi-reads). Samtools flagstat counts each multiple aligment as a different reads, but ezBAMQC counts reads accoriding to the read ID, i.e., each individual read will be counted once no matter that it is a uniquely mapped read or multi-read. \n+\n+Q: What is "Low Quality Reads" ?\n+\n+A: Reads marked as qc fail accoriding to SAM format or reads with mapping quality lower than the value set by the option -q will be considered as "Low Quality Reads".\n+\n+Q: How the setting of option -q alter the results? \n+\n+A: Reads with low quality, i.e., did not pass -q cutoff, are only counted in Total Reads, Mapped Reads, and Mappability by mapping quality plot. The rest of the report does not include low quality reads. \n+\n+Q: Do multi-reads (non-uniquely mapped reads) have been considered in Read distribution and gene quantification?\n+\n+A: No. Only uniquely mapped reads were counted. \n+\n+\n+Acknowledgements\n+================\n+\n+#) Samtools contributors\n+#) Users\' valuable feedback\n+\n+Copying & Distribution\n+======================\n+\n+ezBAMQC is free software: you can redistribute it and/or modify\n+it under the terms of the GNU General Public License as published by\n+the Free Software Foundation, either version 3 of the License, or\n+(at your option) any later version.\n+\n+This program is distributed in the hope that it will be useful,\n+but *WITHOUT ANY WARRANTY*; without even the implied warranty of\n+*MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE*. See the\n+GNU General Public License for more details.\n+\n+You should have received a copy of the GNU General Public License\n+along with ezBAMQC. If not, see `this website <http://www.gnu.org/licenses/>`_\n' |
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| @@ -12,7 +12,7 @@ @status: -@version: 0.6.6 +@version: 0.6.7 ''' @@ -872,7 +872,7 @@ f.write("nz_gene_mm[i] = length(which(M1[,i]>0))/nz_genes * 100 } \n") - f.write("bplt <- barplot(nz_gene_mm,beside=T,border='NA',space=1.5,ylim=c(0,100),ylab='Genes reproducibly detected (%)',col='blue',names.arg=colnames(MM))\n") + f.write("bplt <- barplot(nz_gene_mm,beside=T,border='NA',space=1.5,ylim=c(0,100),ylab='Genes reproducibly detected (%)',col='blue',names.arg=colnames(MM),las=2)\n") f.write("text(y= nz_gene_mm+2, x= bplt, labels=paste(as.character(round(nz_gene_mm,digits=1)),'%',sep=''), xpd=TRUE)\n") @@ -956,7 +956,7 @@ - f.write('barplot(Fn_mm,main="Gene abundance (RPM)",xlab="Sample",ylab="Frequency",col=c("green","blue","red","yellow"),legend=xname)\n') + f.write('barplot(Fn_mm,main="Gene abundance (RPM)",xlab="Sample",ylab="Frequency",col=c("green","blue","red","yellow"),legend=xname,las=2)\n') f.write("dev.state = dev.off()\n") @@ -1022,7 +1022,7 @@ - f.write('barplot(Fn_mm,xlab="Sample",main="Mapping Quality",ylim=c(0,1),ylab="Frequency",col=c("blue","green","yellow","orange","red"),legend=xname)\n') + f.write('barplot(Fn_mm,xlab="Sample",main="Mapping Quality",ylim=c(0,1),ylab="Frequency",col=c("blue","green","yellow","orange","red"),legend=xname,las=2)\n') f.write("dev.state = dev.off()\n") |
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| @@ -89,28 +89,28 @@ sys.exit() BAMQC_HEADER = [ - 'src/bamqc/Constants.h', - 'src/bamqc/Coverage_prof.h', - 'src/bamqc/GeneFeatures.h', - 'src/bamqc/InnerDist_prof.h', - 'src/bamqc/IntervalTree.h', - 'src/bamqc/Mappability.h', - 'src/bamqc/parseBAM.h', - 'src/bamqc/ReadDup_prof.h', - 'src/bamqc/Results.h', - 'src/bamqc/rRNA.h' + 'src/ezBAMQC/Constants.h', + 'src/ezBAMQC/Coverage_prof.h', + 'src/ezBAMQC/GeneFeatures.h', + 'src/ezBAMQC/InnerDist_prof.h', + 'src/ezBAMQC/IntervalTree.h', + 'src/ezBAMQC/Mappability.h', + 'src/ezBAMQC/parseBAM.h', + 'src/ezBAMQC/ReadDup_prof.h', + 'src/ezBAMQC/Results.h', + 'src/ezBAMQC/rRNA.h' ] BAMQC_SOURCE = [ - 'src/bamqc/Coverage_prof.cpp', - 'src/bamqc/GeneFeatures.cpp', - 'src/bamqc/InnerDist_prof.cpp', - 'src/bamqc/IntervalTree.cpp', - 'src/bamqc/Mappability.cpp', - 'src/bamqc/parseBAM.cpp', - 'src/bamqc/ReadDup_prof.cpp', - 'src/bamqc/Results.cpp', - 'src/bamqc/rRNA.cpp' + 'src/ezBAMQC/Coverage_prof.cpp', + 'src/ezBAMQC/GeneFeatures.cpp', + 'src/ezBAMQC/InnerDist_prof.cpp', + 'src/ezBAMQC/IntervalTree.cpp', + 'src/ezBAMQC/Mappability.cpp', + 'src/ezBAMQC/parseBAM.cpp', + 'src/ezBAMQC/ReadDup_prof.cpp', + 'src/ezBAMQC/Results.cpp', + 'src/ezBAMQC/rRNA.cpp' ] ###TODO HAVE TO SPLIT INTO TWO AND MAKE THE A FILE @@ -174,7 +174,7 @@ BAMqc_CFLAGS = ['-fpermissive','-O3','-std=c++11','-Wno-error=declaration-after-statement'] BAMqc_DFLAGS = [('_FILE_OFFSET_BITS','64'),('_LARGEFILE64_SOURCE',''),('_CURSES_LIB','1')] BAMqc_INCLUDES = ['./src/htslib'] -BAMqc_HEADERS = ['./src/bamqc'] +BAMqc_HEADERS = ['./src/ezBAMQC'] BAMqc_EXTRA = ['build/lib.linux-x86_64-2.7/htslib.so'] htslib_CFLAGS = ['-Wno-error=declaration-after-statement'] @@ -182,7 +182,7 @@ htslib_DFLAGS = [('_FILE_OFFSET_BITS','64'),('_USE_KNETFILE','')] setup(name = "ezBAMQC", - version = "0.6.5", + version = "0.6.7", description = 'Quality control tools for NGS alignment file', keywords = 'Quality control BAM file', # make sure to add all the nessacary requires |
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| @@ -1,12 +0,0 @@ -<tables>cat - <!-- Locations of gene model GTFs --> - <table name="gene_GTF_database" comment_char="#"> - <columns>value, name, dbkey, id</columns> - <file path="tool-data/cshl_geneGTF.loc" /> - </table> - <!-- Locations of rRNA BED files for BAMqc --> - <table name="rRNA_BED_database" comment_char="#"> - <columns>value, name, dbkey, id</columns> - <file path="tool-data/cshl_rRNA_BED.loc" /> - </table> -</tables> \ No newline at end of file |
