# HG changeset patch # User pjbriggs # Date 1435661046 14400 # Node ID d9c1f213312428c9015b6b087f39e5f3e4acaa8d Uploaded initial version 0.4.4. diff -r 000000000000 -r d9c1f2133124 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,142 @@ +RnaChipIntegrator: integrated analysis of gene expression and ChIP data +======================================================================= + +Galaxy tool wrappers for running the RnaChipIntegrator program +(http://fls-bioinformatics-core.github.com/RnaChipIntegrator/) for integrated +analyses of gene expression and ChIP data. + +There are two tools available that are built around RnaChipIntegrator: + +- General RnaChipIntegrator tool that allows any peaks to be analysed against + any gene list +- A "cannonical gene" variant which allows ChIP peaks to be analysed against a + list of cannonical genes for different genomes + +Automated installation +====================== + +Installation via the Galaxy Tool Shed will take of installing the tool wrapper +and the RnaChipIntegrator programs, installing the .loc files, and setting the +appropriate environment variables. + +Manual Installation +=================== + +There are three files to install: + +- ``rnachipintegrator_wrapper.xml`` (the Galaxy tool definition for general usage) +- ``rnachipintegrator_canonical_genes.xml`` (tool definition for the "canonical + gene" variant) +- ``rnachipintegrator_wrapper.sh`` (the shell script wrapper) + +The suggested location is in a ``tools/rnachipintegrator/`` folder. You will then +need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool +by adding the lines: + + + + +You will also need to install the RnaChipIntegrator program: + +- http://fls-bioinformatics-core.github.com/RnaChipIntegrator/ + +In addition for the cannonical gene and histone modification variants, it's +necessary to copy the .loc.sample files to .loc Galaxy's ``tool-data`` folder: + +- **Cannonical genes**: its necessary to manually acquire cannonical gene + list files from UCSC and then add appropriate references in the + ``rnachipintegrator_canonical_genes.loc`` file. + +If you want to run the functional tests, copy the sample test files under +``test-data`` to Galaxy's ``test-data/`` directory. Then: + + ./run_tests.sh -id fls_rnachipintegrator_wrapper + + +How to get canonical gene data +============================== + +Getting canonical gene info from UCSC is covered in the screencast at +http://blog.openhelix.eu/?p=6097 + +In summary: + +- **UCSC genome browser:** if multiple versions of each gene are visible (e.g. + if you view 'human Feb 2009 GRCh37/hg19' positions chr17:41,100,000-41,300,000) + then: + + - Scroll down to the Gene & Gene Prediction section + - Click on the UCSC genes link + - Uncheck the tickbox next to splice variants and resubmit to view without + duplicates. + +- **UCSC table browser:** to obtain the canonical set of genes from the table + browser: + + - Select knownCanonical from the table menu + - Select selected fields from primary & related tables from the output format menu + - Click on Get output + - Select the fields of interest (e.g. 'chrom', 'chromStart', 'chromEnd' from the + 'knownCanonical' table plus 'geneSymbol' from the kgXref table.) + - Click on Get output to get the data for download + +(Hint: to also get strand direction information i.e. +/-, also allow selection +from the refGene table, and select the strand field.) + + +Note on Excel output files and Galaxy +===================================== + +RnaChipIntegrator produces an Excel spreadsheet as one of its outputs, +however Galaxy is not currently set up by default to handle these. + +To enable Excel output file handling in Galaxy, edit the ``datatypes_conf.xml`` +file and add: + + + +You'll also need to remove the existing datatype with extension "xls". + +Restarting Galaxy should mean that the browser correctly handles Excel outputs +from RnaChipIntegrator. + +History +======= + +========== ====================================================================== +Version Changes +---------- ---------------------------------------------------------------------- +0.4.4-0 - Initial version pushed to toolshed +========== ====================================================================== + + +Developers +========== + +This tool is developed on the following GitHub repository: +https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use +the ``package_rnachipintegrator_wrapper.sh`` script. + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff -r 000000000000 -r d9c1f2133124 data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.py Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,97 @@ +#!/usr/bin/env python +# + +import sys +import os +import optparse +import shutil + +from galaxy.util.json import from_json_string, to_json_string + +# Download file from specified URL and put into local subdir + +if __name__ == '__main__': + #Parse Command Line + parser = optparse.OptionParser() + options,args = parser.parse_args() + print "options: %s" % options + print "args : %s" % args + if len(args) != 2: + p.error("Need to supply JSON file name and description text") + + # Read the JSON supplied from the data manager tool + # Results from this program will be returned via the + # same file + jsonfile = args[0] + params = from_json_string(open(jsonfile).read() ) + print "%s" % params + + # Extract the data from the input JSON + # See https://wiki.galaxyproject.org/Admin/Tools/DataManagers/HowTo/Define?highlight=%28\bAdmin%2FTools%2FDataManagers\b%29 + # for example of JSON + # + # We want the values set in the data manager XML + dbkey = params['param_dict']['dbkey'] + description = args[1].strip() + identifier = params['param_dict']['unique_id'].strip() + # Where to put the output file + # Nb we have to make this ourselves, it doesn't exist by default + target_dir = params['output_data'][0]['extra_files_path'] + os.mkdir(target_dir) + + method = params['param_dict']['reference_source']['reference_source_selector'] + + # Dictionary for returning to data manager + data_manager_dict = {} + data_manager_dict['data_tables'] = dict() + + if method == 'server': + # Pull in a file from the server + filename = params['param_dict']['reference_source']['gene_list_filename'] + create_symlink = params['param_dict']['reference_source']['create_symlink'] + print "Canonical gene list file name: %s" % filename + print "Create symlink: %s" % create_symlink + target_filename = os.path.join(target_dir,os.path.basename(filename)) + if create_symlink == 'copy_file': + shutil.copyfile(filename,target_filename) + else: + os.symlink(filename,target_filename) + # Check identifier and description + if not description: + description = "%s: %s" % (dbkey, + os.path.splitext(os.path.basename(filename))[0]) + if not identifier: + identifier = "%s_%s" % (dbkey, + os.path.splitext(os.path.basename(filename))[0]) + # Update the output dictionary + data_manager_dict['data_tables']['rnachipintegrator_canonical_genes'] = { + 'value': identifier, + 'dbkey': dbkey, + 'name': description, + 'path': os.path.basename(filename), + } + elif method == 'history': + # Copy file from history + filename = params['param_dict']['reference_source']['input_gene_list'] + target_filename = os.path.join(target_dir,os.path.basename(filename)) + shutil.copyfile(filename,target_filename) + # Check identifier and description + if not description: + description = "%s: %s" % (dbkey, + os.path.splitext(os.path.basename(filename))[0]) + if not identifier: + identifier = "%s_%s" % (dbkey, + os.path.splitext(os.path.basename(filename))[0]) + # Update the output dictionary + data_manager_dict['data_tables']['rnachipintegrator_canonical_genes'] = { + 'value': identifier, + 'dbkey': dbkey, + 'name': description, + 'path': os.path.basename(filename), + } + else: + raise NotImplementedError("Method '%s' not implemented" % method) + + #save info to json file + open(jsonfile,'wb').write(to_json_string(data_manager_dict)) + diff -r 000000000000 -r d9c1f2133124 data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,90 @@ + + Fetch and install canonical gene lists for RnaChipIntegrator + data_manager_rnachipintegrator_fetch_canonical_genes.py + "${out_file}" + "${description}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**What it does** + +Adds a canonical gene list file to the *rnachipintegrator_canonical_genes* +data table, so that it can be used in the *Analyse canonical genes against ChIP +data* tool. + +At present the gene list files must be created manually and placed on the +Galaxy server; see below for information on how to obtain canonical gene lists +from UCSC. + +**Notice:** If you leave the description blank then it will be generated +automatically. + +------ + +.. class:: infomark + +**Obtaining canonical gene lists** + +Getting canonical gene info from UCSC is covered in the screencast at +http://blog.openhelix.eu/?p=6097 + +**UCSC genome browser:** if multiple versions of each gene are visible (e.g. +if you view 'human Feb 2009 GRCh37/hg19' positions chr17:41,100,000-41,300,000) +then: + + - Scroll down to the *Gene & Gene Prediction* section + - Click on the *UCSC genes* link + - Uncheck the tickbox next to *splice variants* and resubmit to view without + duplicates. + +**UCSC table browser:** to obtain the canonical set of genes from the table browser: + + - Select *knownCanonical* from the table menu + - Select selected fields from primary & related tables from the output format menu + - Click on *Get output* + - Select the fields of interest (e.g. 'chrom', 'chromStart', 'chromEnd' from the + 'knownCanonical' table plus 'geneSymbol' from the *kgXref* table.) + - Click on Get output to get the data for download + +**Hint:** to also get strand direction information i.e. +/-, also allow selection +from the refGene table, and select the strand field.) + + diff -r 000000000000 -r d9c1f2133124 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,20 @@ + + + + + + + + + + + ${path} + rnachipintegrator/${dbkey}/${path} + + ${GALAXY_DATA_MANAGER_DATA_PATH}/rnachipintegrator/${dbkey}/${path} + abspath + + + + + diff -r 000000000000 -r d9c1f2133124 rnachipintegrator_canonical_genes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnachipintegrator_canonical_genes.xml Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,235 @@ + + using RnaChipIntegrator + + rnachipintegrator_macros.xml + + + + rnachipintegrator_wrapper.sh + #if str( $analysis_options.peak_type ) == "summits" + #if str( $analysis_options.window ) != "" + --window=$analysis_options.window + #end if + #if str( $analysis_options.cutoff ) != "" + --cutoff=$analysis_options.cutoff + #end if + #end if + #if str( $analysis_options.peak_type ) == "regions" + #if str( $analysis_options.edge_cutoff ) != "" + --edge-cutoff=$analysis_options.edge_cutoff + #end if + #if str( $analysis_options.number ) != "" + --number=$analysis_options.number + #end if + #if (str( $analysis_options.promoter_start ) != "" and str( $analysis_options.promoter_end )) + --promoter_region=$analysis_options.promoter_start,$analysis_options.promoter_end + #end if + #if $analysis_options.pad_output + --pad + #end if + #end if + ${canonical_genes.fields.path} $chipseq + --output_xls $xls_output + #if $results_as_zip + --zip_file $zip_file + #else + #if str( $analysis_options.peak_type ) == "summits" + --summit_outputs $peaks_to_transcripts_out $tss_to_summits_out + #end if + #if str( $analysis_options.peak_type ) == "regions" + --peak_outputs $transcripts_to_edges_out + $transcripts_to_edges_summary + $tss_to_edges_out + $tss_to_edges_summary + #end if + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + analysis_options['peak_type'] == "summits" + results_as_zip is False + + + analysis_options['peak_type'] == "summits" + results_as_zip is False + + + + analysis_options['peak_type'] == "regions" + results_as_zip is False + + + analysis_options['peak_type'] == "regions" + results_as_zip is False + + + analysis_options['peak_type'] == "regions" + results_as_zip is False + + + analysis_options['peak_type'] == "regions" + results_as_zip is False + + + results_as_zip is True + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**What it does** + +Run RnaChipIntegrator to analyse ChIP data against a set of list of "canonical +genes" for a specific organism/genome build, identifying the nearest ChIP peaks +to each cannonical gene (vice versa). + +For ChIP peaks defined as regions the following analyses are performed: + + * **TranscriptsToPeakEdges**: reports the nearest transcripts with the smallest + distance from either their TSS or TES to the nearest peak edge. + + * **TSSToPeakEdges**: reports the nearest transcripts with the smallest distance + from their TSS to the nearest peak edge. + +For ChIP peaks defined as summits: + + * **TSSToSummits**: reports the nearest transcripts with the smallest distance + from the TSS to the nearest peak summit. + + * **PeaksToTranscripts**: reports the nearest peak summits with the smallest + distance to either the TSS or TES of each transcript. + +RnaChipIntgerator can be obtained from +http://fls-bioinformatics-core.github.com/RnaChipIntegrator/ + +------------- + +.. class:: infomark + +**Input** + +The ChIP-seq data must be in a tab-delimited file with 3 columns of data for each +ChIP peak (one per line): + +====== ========== ====================================================================== +Column Name Description +====== ========== ====================================================================== + 1 chr Chromosome name (must match one of those in expression data file) + 2 start Start position of the peak + 3 end End position of the peak (start + 1 for summit data) +====== ========== ====================================================================== + +The ChIP peak data can be either the summit (in which case 'end' - 'start' = 1) or the +entire extent of the binding region (with 'start' and 'end' indicating the limits). + +------------- + +.. class:: infomark + +**Output** + +The outputs from this tool vary depending on the type of ChIP data that is input (i.e +summits or peaks), however generally there is one tab-delimited results file for each +analysis described above in the **What it does** section (some analyses output a second +file with just the "best" hits). + +A history item will be generated for each output file, unless the option to put them +into a single zip archive is selected; this archive file will have to be downloaded +and unzipped on your local machine. It is recommended that you refer to the +RnaChipIntegrator documentation for information on the contents of each output file: +https://github.com/fls-bioinformatics-core/RnaChipIntegrator/blob/master/doc/MANUAL.markdown + +In addition an Excel spreadsheet (with one page for each analysis performed) is always +produced. + +------------- + +.. class:: infomark + +**Credits** + +This Galaxy tool has been developed within the Bioinformatics Core Facility at the +University of Manchester. It runs the RnaChipIntegrator package which has also been +developed by this group, and is documented at +http://fls-bioinformatics-core.github.com/RnaChipIntegrator/ + +Please kindly acknowledge the Bioinformatics Core Facility if you use this tool. + + diff -r 000000000000 -r d9c1f2133124 rnachipintegrator_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnachipintegrator_macros.xml Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,14 @@ + + 0.4.4 + + + python_xlwt + python_xlrd + python_xlutils + rnachipintegrator + + + + rnachipintegrator --version + + diff -r 000000000000 -r d9c1f2133124 rnachipintegrator_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnachipintegrator_wrapper.sh Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,137 @@ +#!/bin/sh +# +# Wrapper script to run RnaChipIntegrator as a Galaxy tool +# +# usage: sh rnachipintegrator_wrapper.sh [OPTIONS] --output_xls +# +echo RnaChipIntegrator: analyse gene expression and ChIP data +# +# Collect command line options +opts= +output_xls= +peaks_to_transcripts_out= +zip_file= +while [ ! -z "$1" ] ; do + case $1 in + --output_xls) + shift; output_xls=$1 + ;; + --summit_outputs) + shift; peaks_to_transcripts_out=$1 + shift; tss_to_summits_out=$1 + ;; + --peak_outputs) + shift; transcripts_to_edges_out=$1 + shift; transcripts_to_edges_summary=$1 + shift; tss_to_edges_out=$1 + shift; tss_to_edges_summary=$1 + ;; + --zip_file) + shift; zip_file=$1 + ;; + *) + opts="$opts $1" + ;; + esac + shift +done +# +# Run RnaChipIntegrator +# NB append stderr to stdout otherwise Galaxy job will fail +# Direct output to a temporary directory +outdir=`mktemp -d` +base_name=galaxy +cmd="RnaChipIntegrator.py --project=${outdir}/${base_name} $opts" +echo $cmd +$cmd 2>&1 +# +# Check exit code +exit_status=$? +if [ "$exit_status" -ne "0" ] ; then + echo RnaChipIntegrator exited with non-zero status >&2 + # Clean up and exit + /bin/rm -rf $outdir + exit $exit_status +fi +# +# Deal with output files - XLS +if [ -f "${outdir}/${base_name}.xls" ] ; then + /bin/mv ${outdir}/${base_name}.xls $output_xls +else + echo No file ${outdir}/${base_name}.xls >&2 + # Clean up and exit + /bin/rm -rf $outdir + exit 1 +fi +# +# Zip file +if [ ! -z "$zip_file" ] ; then + for ext in "PeaksToTranscripts" "TSSToSummits" "TranscriptsToPeakEdges" "TranscriptsToPeakEdges_summary" "TSSToPeakEdges" "TSSToPeakEdges_summary" ; do + txt_file=${outdir}/${base_name}_${ext}.txt + if [ -f "$txt_file" ] ; then + zip -j -g ${outdir}/archive.zip $txt_file + fi + done + /bin/mv ${outdir}/archive.zip $zip_file +fi +# +# Peaks to transcripts +if [ ! -z "$peaks_to_transcripts_out" ] ; then + outfile=${outdir}/${base_name}_PeaksToTranscripts.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $peaks_to_transcripts_out + else + echo No file $outfile >&2 + fi +fi +# +# TSS to summits +if [ ! -z "$tss_to_summits_out" ] ; then + outfile=${outdir}/${base_name}_TSSToSummits.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $tss_to_summits_out + else + echo No file $outfile >&2 + fi +fi +# +# Transcripts to Peak Edges +if [ ! -z "$transcripts_to_edges_out" ] ; then + outfile=${outdir}/${base_name}_TranscriptsToPeakEdges.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $transcripts_to_edges_out + else + echo No file $outfile >&2 + fi +fi +if [ ! -z "$transcripts_to_edges_summary" ] ; then + outfile=${outdir}/${base_name}_TranscriptsToPeakEdges_summary.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $transcripts_to_edges_summary + else + echo No file $outfile >&2 + fi +fi +# +# TSS to Peak Edges +if [ ! -z "$tss_to_edges_out" ] ; then + outfile=${outdir}/${base_name}_TSSToPeakEdges.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $tss_to_edges_out + else + echo No file $outfile >&2 + fi +fi +if [ ! -z "$tss_to_edges_summary" ] ; then + outfile=${outdir}/${base_name}_TSSToPeakEdges_summary.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $tss_to_edges_summary + else + echo No file $outfile >&2 + fi +fi +# +# Clean up +/bin/rm -rf $outdir +# +# Done diff -r 000000000000 -r d9c1f2133124 rnachipintegrator_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rnachipintegrator_wrapper.xml Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,262 @@ + + + Integrated analysis of gene expression data and ChIP data + + rnachipintegrator_macros.xml + + + + rnachipintegrator_wrapper.sh + #if str( $analysis_options.peak_type ) == "summits" + #if str( $analysis_options.window ) != "" + --window=$analysis_options.window + #end if + #if str( $analysis_options.cutoff ) != "" + --cutoff=$analysis_options.cutoff + #end if + #end if + #if str( $analysis_options.peak_type ) == "regions" + #if str( $analysis_options.edge_cutoff ) != "" + --edge-cutoff=$analysis_options.edge_cutoff + #end if + #if str( $analysis_options.number ) != "" + --number=$analysis_options.number + #end if + #if (str( $analysis_options.promoter_start ) != "" and str( $analysis_options.promoter_end )) + --promoter_region=$analysis_options.promoter_start,$analysis_options.promoter_end + #end if + #if $analysis_options.pad_output + --pad + #end if + #end if + $rnaseq $chipseq + --output_xls $xls_output + #if $results_as_zip + --zip_file $zip_file + #else + #if str( $analysis_options.peak_type ) == "summits" + --summit_outputs $peaks_to_transcripts_out $tss_to_summits_out + #end if + #if str( $analysis_options.peak_type ) == "regions" + --peak_outputs $transcripts_to_edges_out + $transcripts_to_edges_summary + $tss_to_edges_out + $tss_to_edges_summary + #end if + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + analysis_options['peak_type'] == "summits" + results_as_zip is False + + + analysis_options['peak_type'] == "summits" + results_as_zip is False + + + + analysis_options['peak_type'] == "regions" + results_as_zip is False + + + analysis_options['peak_type'] == "regions" + results_as_zip is False + + + analysis_options['peak_type'] == "regions" + results_as_zip is False + + + analysis_options['peak_type'] == "regions" + results_as_zip is False + + + results_as_zip is True + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**What it does** + +Run RnaChipIntegrator to perform integrated analyses of gene expression +and ChIP data, identifying the nearest ChIP peaks to each transcript +and vice versa. + +For ChIP peaks defined as regions the following analyses are performed: + + * **TranscriptsToPeakEdges**: reports the nearest transcripts with the smallest + distance from either their TSS or TES to the nearest peak edge. + + * **TSSToPeakEdges**: reports the nearest transcripts with the smallest distance + from their TSS to the nearest peak edge. + +For ChIP peaks defined as summits: + + * **TSSToSummits**: reports the nearest transcripts with the smallest distance + from the TSS to the nearest peak summit. + + * **PeaksToTranscripts**: reports the nearest peak summits with the smallest + distance to either the TSS or TES of each transcript. + +The program was originally written specifically for ChIP-Seq and RNA-Seq data +but works equally well for ChIP-chip and microarray expression data, and can +also be used to integrate any set of genomic features (e.g. canonical genes, +CpG islands) with expression data. + +RnaChipIntgerator can be obtained from +http://fls-bioinformatics-core.github.com/RnaChipIntegrator/ + +------------- + +.. class:: infomark + +**Input** + +The expression data must be in a tab-delimited file with the following columns +of data for each genomic feature (one feature per line): + +====== ========== ====================================================================== +Column Name Description +====== ========== ====================================================================== + 1 ID Name used to identify the feature in the output + 2 chr Chromosome name + 3 start Start position of the feature + 4 end End position of the feature + 5 strand Must be either '+' or '-' + 6 diff_expr Optional: indicates feature is differentially expressed (1) or not (0) +====== ========== ====================================================================== + +The ChIP-seq data must be in a tab-delimited file with 3 columns of data for each +ChIP peak (one per line): + +====== ========== ====================================================================== +Column Name Description +====== ========== ====================================================================== + 1 chr Chromosome name (must match one of those in expression data file) + 2 start Start position of the peak + 3 end End position of the peak (start + 1 for summit data) +====== ========== ====================================================================== + +The ChIP peak data can be either the summit (in which case 'end' - 'start' = 1) or the +entire extent of the binding region (with 'start' and 'end' indicating the limits). + +------------- + +.. class:: infomark + +**Output** + +The outputs from this tool vary depending on the type of data that is input, however +generally there is one tab-delimited results file for each analysis described above +in the **What it does** section (some analyses output a second file with just the +"best" hits). + +A history item will be generated for each output file, unless the option to put them +into a single zip archive is selected; this archive file will have to be downloaded +and unzipped on your local machine. It is recommended that you refer to the +RnaChipIntegrator documentation for information on the contents of each output file: +https://github.com/fls-bioinformatics-core/RnaChipIntegrator/blob/master/doc/MANUAL.markdown + +In addition an Excel spreadsheet (with one page for each analysis performed) is always +produced. + +------------- + +.. class:: infomark + +**Credits** + +This Galaxy tool has been developed within the Bioinformatics Core Facility at the +University of Manchester. It runs the RnaChipIntegrator package which has also been +developed by this group, and is documented at +http://fls-bioinformatics-core.github.com/RnaChipIntegrator/ + +Please kindly acknowledge the Bioinformatics Core Facility if you use this tool. + + diff -r 000000000000 -r d9c1f2133124 test-data/ChIP_peaks.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ChIP_peaks.txt Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,70 @@ +#peak s e +chr1 10617233 10617437 +chr1 108747519 108747791 +chr1 120760212 120760461 +chr1 132950929 132951247 +chr1 133114860 133115015 +chr1 135582677 135582828 +chr1 135851853 135852218 +chr1 136956468 136956598 +chr1 13829227 13829564 +chr1 138437726 138437860 +chr1 140381656 140381785 +chr1 145591041 145591176 +chr1 154971572 154971673 +chr1 155123313 155123435 +chr1 158510523 158510813 +chr1 158537267 158537411 +chr1 158580638 158580759 +chr1 158835251 158835391 +chr1 159240736 159240866 +chr1 163827897 163828062 +chr1 164215623 164215935 +chr1 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+1,957 @@ +#RefSeq_Gene Symbol chr1 start stop strand diff_exp +AF064749_Col6a3 chr1 92566771 92800755 - 1 +AK015559_4930472D16Rik chr1 25020851 25021989 - 1 +AK030377_A330023F24Rik chr1 196781953 196826186 - 1 +AK080193_A530079E22Rik chr1 89401837 89403491 - 1 +AK082264_C230030N03Rik chr1 34735043 34781084 + 1 +BC006931_AI597479 chr1 43153807 43172843 + 1 +BC021773_Glb1l chr1 75193364 75207353 - 1 +BC023951_D1Ertd622e chr1 99540054 99558631 - 1 +BC028767_3110009E18Rik chr1 122017764 122114603 + 1 +BC031781_BC031781 chr1 182781250 182798240 + 1 +BC034187_BC035947 chr1 78493611 78497758 - 1 +BC043098_Fam168b chr1 34870072 34917183 - 1 +BC049091_D1Bwg0212e chr1 39592545 39603734 + 1 +BC049713_Ankrd45 chr1 163072817 163099826 + 1 +BC050813_4921511C04Rik chr1 37157481 37244861 + 1 +BC051128_4921521F21Rik chr1 65059273 65079312 - 1 +BC052693_2810422O20Rik chr1 165924541 165927371 + 1 +BC052931_A630001G21Rik chr1 87601462 87674840 - 1 +BC053100_5730559C18Rik chr1 138110108 138130841 - 1 +BC054802_9630058J23Rik chr1 181476521 181558044 + 1 +BC055845_2810025M15Rik chr1 159342483 159350353 + 1 +BC055955_A130010J15Rik chr1 194999663 195004015 + 1 +BC057872_Rab3gap2 chr1 187028006 187110623 + 1 +BC058417_2610017I09Rik chr1 42648822 42751667 - 1 +BC059254_Phlpp chr1 108042052 108306367 + 1 +BC070435_Fam123c chr1 34620070 34671545 + 1 +BC070446_Fam135a chr1 24017617 24107170 - 1 +BC071241_9430016H08Rik chr1 57463192 57497936 + 1 +BC072639_2010300C02Rik chr1 37646877 37776659 - 1 +BC080290_5033414K04Rik chr1 84032539 84360735 - 0 +BC082310_9430031J16Rik chr1 81073525 81338329 + 0 +BC089525_2310007B03Rik chr1 95047933 95063386 - 0 +BC089561_Cep350 chr1 157692096 157820375 - 0 +BC147491_A230074B11Rik chr1 37083441 37133840 + 0 +BC147657_9630028B13Rik chr1 187253234 187265698 - 0 +ENSMUST00000027997_Rgs5 chr1 171625108 171625913 + 0 +ENSMUST00000051203_1700001G17Rik chr1 33726669 33727551 + 0 +ENSMUST00000054333_A130050O07Rik chr1 139823828 139826840 + 0 +ENSMUST00000056879_C230029F24Rik chr1 49301475 49397265 + 0 +ENSMUST00000057543_A730013G03Rik chr1 194659323 194661397 - 0 +ENSMUST00000062637_4930470H14Rik chr1 175156866 175201240 + 0 +ENSMUST00000070048_ENSMUSG00000056128 chr1 92571736 92576368 + 0 +ENSMUST00000070987_EG433384 chr1 183781705 183783320 - 0 +ENSMUST00000072395_Olfr1406 chr1 175113651 175120746 - 0 +ENSMUST00000094288_Wdr64 chr1 177654798 177798070 + 0 +ENSMUST00000094950_Pgap1 chr1 54529849 54614539 - 0 +ENSMUST00000097776_Cnnm3 chr1 36567938 36585164 + 0 +EU429481_Igfn1 chr1 137825893 137890307 - 0 +FJ024495_Ildr2 chr1 168236882 168239692 - 0 +FJ210934_Unc80 chr1 66514856 66556109 + 0 +NM_001001565_Chpf chr1 75470923 75476437 - 0 +NM_001001809_Olfr218 chr1 175130421 175134469 + 0 +NM_001001883_Hecw2 chr1 53867026 54252002 - 0 +NM_001003917_Atg9a chr1 75177439 75189181 - 0 +NM_001004173_Sgpp2 chr1 78306692 78416864 + 0 +NM_001005423_Mreg chr1 72170192 72258895 - 0 +NM_001005507_Smg7 chr1 154684125 154750410 - 0 +NM_001005508_Arhgap30 chr1 173319072 173340822 + 0 +NM_001005520_Olfr244 chr1 176032571 176067605 - 0 +NM_001008419_Aox3l1 chr1 58335180 58437083 + 0 +NM_001008426_EG433365 chr1 155721475 155724001 + 0 +NM_001008533_Adora1 chr1 136095799 136181661 - 0 +NM_001009940_Il19 chr1 132786042 132915234 - 0 +NM_001011525_Olfr1415 chr1 94376258 94381054 - 0 +NM_001011525_Olfr1415 chr1 94407669 94418761 - 0 +NM_001011684_Nms chr1 38995917 39007113 + 0 +NM_001011873_Xkr9 chr1 13658862 13691794 + 0 +NM_001011874_Xkr4 chr1 3203722 3713108 - 0 +NM_001012330_Zfp238 chr1 179359958 179380892 + 0 +NM_001013374_Lman2l chr1 36362897 36502078 - 0 +NM_001013382_Lrrc52 chr1 169375806 169397136 - 0 +NM_001013771_Gm973 chr1 59573136 59693241 + 0 +NM_001013779_Aim2 chr1 175385835 175396165 + 0 +NM_001014974_Ttll4 chr1 74708314 74748400 + 0 +NM_001024721_BC094916 chr1 175451304 175466101 - 0 +NM_001024945_Qsox1 chr1 157625296 157670499 - 0 +NM_001025156_Ccdc93 chr1 123208865 123403037 + 0 +NM_001025565_Lhx9 chr1 140694768 140740509 - 0 +NM_001025602_Il1rl1 chr1 40462708 40522260 + 0 +NM_001029984_Fcrlb chr1 172836813 172843072 - 0 +NM_001037170_Tomm40l chr1 173147934 173152645 - 0 +NM_001037725_Fam117b chr1 59937517 60042190 + 0 +NM_001037918_Lipt1 chr1 37928603 37934232 + 0 +NM_001037999_Dbi chr1 122009883 122046068 - 0 +NM_001038592_Glrx2 chr1 145585774 145608282 + 0 +NM_001038619_Dnm3 chr1 163902671 164408155 - 0 +NM_001039126_Asb1 chr1 93437143 93461729 + 0 +NM_001039472_Kif21b chr1 138027986 138074578 + 0 +NM_001039475_Slco6b1 chr1 98802763 98894139 - 0 +NM_001039482_Klhl20 chr1 163018528 163061699 - 0 +NM_001039483_Tmco1 chr1 169238419 169279112 + 0 +NM_001039484_Kcnj10 chr1 174258852 174304216 + 0 +NM_001039493_Plekhm3 chr1 64832557 65032270 - 0 +NM_001039495_Ccdc108 chr1 74947239 74982168 - 0 +NM_001039509_Pnkd chr1 74331504 74400245 + 0 +NM_001039710_Coq10b chr1 55101051 55129538 + 0 +NM_001039934_Mtap2 chr1 66187374 66489157 + 0 +NM_001042634_Clk1 chr1 58467034 58480936 - 0 +NM_001045481_Ifi203 chr1 175804708 175928457 - 0 +NM_001077189_Fcgr2b chr1 172890316 172916060 - 0 +NM_001077353_Gsta3 chr1 21230690 21255722 + 0 +NM_001077403_Nrp2 chr1 62724499 63100251 + 0 +NM_001081023_Cacna1s chr1 137949297 138016348 + 0 +NM_001081078_Lct chr1 130174327 130224881 - 0 +NM_001081079_Ogfrl1 chr1 23278472 23451348 - 0 +NM_001081259_Mfsd7b chr1 192825304 192850534 - 0 +NM_001081275_1700009P17Rik chr1 173032694 173057075 + 0 +NM_001081361_Mosc1 chr1 186610666 186635172 - 0 +NM_001081756_E030049G20Rik chr1 128277776 128727190 - 0 +NM_001082573_Crygc chr1 65118108 65146863 - 0 +NM_001083897_Mpzl1 chr1 167522314 167564669 - 0 +NM_001085409_Steap3 chr1 122037552 122169282 - 0 +NM_001099637_Cep170 chr1 178663793 178744307 - 0 +NM_001103182_Lin9 chr1 182572002 182620816 + 0 +NM_001105667_Dtymk chr1 95689006 95698492 - 0 +NM_001110783_Ank1 chr1 77759424 77766452 - 0 +NM_001110831_Dnpep chr1 75304471 75314673 - 0 +NM_001111059_Cd34 chr1 196683888 196826273 + 0 +NM_001111279_Wdfy1 chr1 79689958 79772698 - 0 +NM_001111314_Ngef chr1 89373415 89470499 - 0 +NM_001111316_Ptprc chr1 139959456 140088994 - 0 +NM_001111320_Idh1 chr1 65185668 65233033 - 0 +NM_001113394_Cd247 chr1 167711216 167807397 + 0 +NM_001122685_Rhbdd1 chr1 82313047 82441937 + 0 +NM_001126046_Fam178b chr1 36619544 36740008 - 0 +NM_001128605_Psen2 chr1 182157140 182247499 - 0 +NM_001128609_Dedd chr1 173258959 173273620 + 0 +NM_001130174_Tnnt2 chr1 137732931 137748838 + 0 +NM_001134829_Lpgat1 chr1 193521144 193605705 + 0 +NM_001136070_Lgtn chr1 133049773 133084235 + 0 +NM_001142647_Tmem194b chr1 52687569 52708760 + 0 +NM_001159649_Lax1 chr1 135575626 135586665 - 0 +NM_001159719_Sept2 chr1 95375046 95406820 + 0 +NM_001159730_Pdc chr1 152154402 152181077 + 0 +NM_007381_Acadl chr1 66861363 66909886 - 0 +NM_007415_Parp1 chr1 182499033 182531385 + 0 +NM_007422_Adss chr1 179693113 179888685 - 0 +NM_007432_Akp3 chr1 89021583 89042994 + 0 +NM_007433_Akp5 chr1 88983274 88986861 - 0 +NM_007453_Prdx6 chr1 163170243 163210238 - 0 +NM_007463_Speg chr1 75371872 75428879 + 0 +NM_007495_Astn1 chr1 160292424 160626748 + 0 +NM_007498_Atf3 chr1 192994178 193057173 - 0 +NM_007525_Bard1 chr1 71076934 71149526 - 0 +NM_007561_Bmpr2 chr1 59820296 59927706 + 0 +NM_007570_Btg2 chr1 135971251 135991759 - 0 +NM_007576_C4bp chr1 132531357 132558199 - 0 +NM_007642_Cd28 chr1 60763315 60830749 + 0 +NM_007649_Cd48 chr1 173603288 173635385 + 0 +NM_007685_Cfc1 chr1 34592493 34601156 + 0 +NM_007695_Chi3l1 chr1 136069840 136086738 + 0 +NM_007722_Cxcr7 chr1 92100063 92112863 + 0 +NM_007733_Col19a1 chr1 24258667 24602262 - 0 +NM_007734_Col4a3 chr1 82583506 82718629 + 0 +NM_007735_Col4a4 chr1 82438140 82584744 - 0 +NM_007737_Col5a2 chr1 45431177 45560226 - 0 +NM_007740_Col9a1 chr1 24164692 24268636 + 0 +NM_007758_Cr2 chr1 196963005 197003002 - 0 +NM_007768_Crp chr1 174620782 174763152 + 0 +NM_007774_Cryga chr1 65146986 65150012 - 0 +NM_007776_Crygd chr1 65108417 65110024 - 0 +NM_007777_Cryge chr1 65095133 65097767 - 0 +NM_007791_Csrp1 chr1 137526251 137648807 + 0 +NM_007799_Ctse chr1 133534879 133572077 + 0 +NM_007827_Daf2 chr1 132285116 132319576 - 0 +NM_007842_Dhx9 chr1 155302618 155334755 - 0 +NM_007853_Degs1 chr1 184205901 184212915 - 0 +NM_007921_Elf3 chr1 137149649 137155139 - 0 +NM_007923_Elk4 chr1 133904204 133929189 + 0 +NM_007936_Epha4 chr1 77280640 77511653 - 0 +NM_007955_Ptprv chr1 137004306 137029151 - 0 +NM_007976_F5 chr1 166081877 166150388 + 0 +NM_008030_Fmo3 chr1 164883934 164914811 - 0 +NM_008057_Fzd7 chr1 59538966 59546428 + 0 +NM_008059_G0s2 chr1 195098362 195108977 - 0 +NM_008131_Glul chr1 155746721 155757023 + 0 +NM_008132_Glrp1 chr1 90396446 90406631 - 0 +NM_008209_Mr1 chr1 156951231 157006024 - 0 +NM_008210_H3f3a chr1 182694052 182744054 - 0 +NM_008250_Hlx chr1 186542564 186592227 - 0 +NM_008288_Hsd11b1 chr1 195047814 195090228 - 0 +NM_008299_Dnajb3 chr1 90101307 90102337 - 0 +NM_008311_Htr2b chr1 87995611 88008576 - 0 +NM_008327_Ifi202b chr1 175892699 175912872 - 0 +NM_008329_Ifi204 chr1 175677424 175929523 - 0 +NM_008342_Igfbp2 chr1 72840313 72899038 + 0 +NM_008362_Il1r1 chr1 40274145 40373439 + 0 +NM_008365_Il18r1 chr1 40522407 40557703 + 0 +NM_008384_Inpp1 chr1 52826936 52890006 - 0 +NM_008429_Kcnj9 chr1 174250632 174259434 - 0 +NM_008440_Kif1a chr1 94912041 94998420 - 0 +NM_008484_Lamb3 chr1 195033913 195170047 + 0 +NM_008485_Lamc2 chr1 154969890 155033557 - 0 +NM_008510_Xcl1 chr1 166861801 166916999 - 0 +NM_008515_Lrrfip1 chr1 92895314 93025509 + 0 +NM_008534_Ly9 chr1 173518153 173537531 - 0 +NM_008551_Mapkapk2 chr1 132950274 133013820 - 0 +NM_008563_Mcm3 chr1 20792654 20810343 - 0 +NM_008567_Mcm6 chr1 130228167 130256262 - 0 +NM_008575_Mdm4 chr1 134877138 134927144 - 0 +NM_008623_Mpz chr1 173081953 173091254 + 0 +NM_008651_Mybl1 chr1 9635825 9690280 - 0 +NM_008667_Nab1 chr1 52487127 52611216 - 0 +NM_008678_Ncoa2 chr1 13129206 13399268 - 0 +NM_008696_Map4k4 chr1 39958025 40102235 + 0 +NM_008719_Npas2 chr1 39250631 39420071 + 0 +NM_008763_Olfr16 chr1 174886928 174887857 + 0 +NM_008765_Orc2l chr1 58519275 58561933 - 0 +NM_008781_Pax3 chr1 78047196 78193701 - 0 +NM_008795_Pctk3 chr1 133972174 134036519 - 0 +NM_008798_Pdcd1 chr1 95931620 95977526 - 0 +NM_008801_Pde6d chr1 88427331 88479102 - 0 +NM_008825_Pfkfb2 chr1 132566787 132625820 - 0 +NM_008866_Lypla1 chr1 4797815 4844373 + 0 +NM_008869_Pla2g4a chr1 151661289 151808414 - 0 +NM_008882_Plxna2 chr1 196411150 196654445 + 0 +NM_008900_Pou3f3 chr1 42662066 42757055 + 0 +NM_008911_Ppox chr1 173200042 173211335 - 0 +NM_008922_Prim2 chr1 33510658 33727287 - 0 +NM_008937_Prox1 chr1 191943166 191999411 - 0 +NM_008976_Ptpn14 chr1 191512039 191694746 + 0 +NM_008985_Ptprn chr1 75243625 75261057 - 0 +NM_008998_Rab17 chr1 92842177 92905581 - 0 +NM_008999_Rab23 chr1 33776747 33799402 + 0 +NM_009049_Resp18 chr1 75268774 75274970 - 0 +NM_009061_Rgs2 chr1 145846468 145858945 - 0 +NM_009062_Rgs4 chr1 171671620 171743114 - 0 +NM_009063_Rgs5 chr1 171585632 171625107 + 0 +NM_009107_Rxrg chr1 169399669 169569753 + 0 +NM_009118_Sag chr1 89700275 89741733 + 0 +NM_009126_Serpinb3a chr1 108942184 108948902 - 0 +NM_009129_Scg2 chr1 79431244 79436675 - 0 +NM_009183_St8sia4 chr1 97484259 97672426 - 0 +NM_009190_Vps4b chr1 108665873 108739123 - 0 +NM_009208_Slc4a3 chr1 75539833 75564973 + 0 +NM_009230_Soat1 chr1 158354679 158417632 - 0 +NM_009255_Serpine2 chr1 79778648 79891246 - 0 +NM_009257_Serpinb5 chr1 108757652 108779925 + 0 +NM_009283_Stat1 chr1 51740305 52218707 + 0 +NM_009307_Syt2 chr1 136543209 136659150 + 0 +NM_009334_Tcfap2b chr1 19198995 19228906 + 0 +NM_009352_Terf1 chr1 15785995 15845901 + 0 +NM_009355_Tesp1 chr1 34554997 34559905 + 0 +NM_009356_Tesp2 chr1 34594321 34617749 - 0 +NM_009367_Tgfb2 chr1 188337162 188544530 - 0 +NM_009399_Tnfrsf11a chr1 107677300 107859295 + 0 +NM_009407_Tnp1 chr1 73061657 73062512 - 0 +NM_009418_Tpp2 chr1 43936027 44065003 + 0 +NM_009447_Tuba4a chr1 75210818 75219831 - 0 +NM_009452_Tnfsf4 chr1 163212600 163374314 + 0 +NM_009460_Sumo1 chr1 59643412 59727658 - 0 +NM_009480_Usf1 chr1 173341335 173348954 + 0 +NM_009509_Vil1 chr1 74455970 74485488 + 0 +NM_009518_Wnt10a chr1 74838090 74898253 + 0 +NM_009526_Wnt6 chr1 74818493 74831875 + 0 +NM_009533_Xrcc5 chr1 72354001 72453365 + 0 +NM_009539_Zap70 chr1 36818663 36839663 + 0 +NM_009579_Slc30a1 chr1 193730666 193737101 + 0 +NM_009581_Zp3r chr1 132473290 132526179 - 0 +NM_009604_Chrng chr1 89102267 89109269 + 0 +NM_009676_Aox1 chr1 58086687 58165423 + 0 +NM_009721_Atp1b1 chr1 166367243 166524675 - 0 +NM_009741_Bcl2 chr1 108362593 108614036 - 0 +NM_009782_Cacna1e chr1 156242220 156916799 - 0 +NM_009786_Cacybp chr1 162132500 162143003 - 0 +NM_009791_Aspm chr1 141351360 141393207 + 0 +NM_009794_Capn2 chr1 184394108 184479307 - 0 +NM_009803_Nr1i3 chr1 173122612 173149661 + 0 +NM_009812_Casp8 chr1 58818409 58904327 + 0 +NM_009813_Casq1 chr1 174140028 174150006 - 0 +NM_009826_Rb1cc1 chr1 6196277 6266709 + 0 +NM_009843_Ctla4 chr1 60943864 61098205 + 0 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16530881 16609419 - 0 +NM_025784_Bcs1l chr1 74634010 74639375 + 0 +NM_025819_1200016B10Rik chr1 153214763 153304502 - 0 +NM_025864_Tmem206 chr1 193149566 193176819 + 0 +NM_025867_Serpinb11 chr1 109246610 109277052 + 0 +NM_025920_Thap4 chr1 95602021 95651542 - 0 +NM_025964_Fam119a chr1 64653048 64670990 - 0 +NM_026024_Ube2t chr1 136857731 136870739 + 0 +NM_026041_Rrp15 chr1 188544857 188573732 - 0 +NM_026078_Pigc chr1 163860747 163957217 + 0 +NM_026123_Unc50 chr1 37486671 37504876 + 0 +NM_026171_Nvl chr1 183008557 183074318 - 0 +NM_026187_Ankzf1 chr1 75188977 75192143 + 0 +NM_026187_Ankzf1 chr1 75192524 75195962 + 0 +NM_026195_Atic chr1 71584010 71626205 + 0 +NM_026234_Pigm chr1 174306609 174314210 + 0 +NM_026241_Ankrd39 chr1 36594353 36604077 - 0 +NM_026250_Zh2c2 chr1 99658035 99706130 + 0 +NM_026321_Fam174a chr1 97174825 97346168 + 0 +NM_026367_Gpatch2 chr1 189010707 189180483 + 0 +NM_026369_Arpc5 chr1 154613024 154638792 + 0 +NM_026375_Ahctf1 chr1 181675025 181733948 - 0 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116788050 116788051 +chr1 117105699 117105700 +chr1 117651574 117651575 +chr1 117666069 117666070 +chr1 118378031 118378032 +chr1 119053534 119053535 +chr1 119113385 119113386 +chr1 119174525 119174526 +chr1 119503762 119503763 +chr1 119527726 119527727 +chr1 119948214 119948215 +chr1 120267925 120267926 +chr1 120380981 120380982 +chr1 120465310 120465311 +chr1 120797706 120797707 +chr1 121041195 121041196 +chr1 121094948 121094949 +chr1 121167893 121167894 +chr1 121340746 121340747 +chr1 121587267 121587268 +chr1 121681260 121681261 +chr1 121816202 121816203 +chr1 123026661 123026662 +chr1 123170986 123170987 +chr1 123685384 123685385 +chr1 123835178 123835179 +chr1 123920817 123920818 +chr1 123949970 123949971 +chr1 124461424 124461425 +chr1 125400371 125400372 +chr1 126171930 126171931 +chr1 126179030 126179031 +chr1 126687579 126687580 +chr1 126712327 126712328 +chr1 126783497 126783498 +chr1 126787012 126787013 +chr1 126963082 126963083 +chr1 127190153 127190154 +chr1 127228396 127228397 +chr1 127507342 127507343 +chr1 127703188 127703189 +chr1 127735504 127735505 +chr1 128049231 128049232 +chr1 128388917 128388918 +chr1 128791747 128791748 +chr1 129571914 129571915 +chr1 129582844 129582845 +chr1 130923911 130923912 +chr1 131245002 131245003 +chr1 131624212 131624213 +chr1 131653028 131653029 +chr1 131673494 131673495 +chr1 131762457 131762458 +chr1 132812150 132812151 +chr1 133122490 133122491 +chr1 133337646 133337647 +chr1 134107973 134107974 +chr1 134516117 134516118 +chr1 134650852 134650853 +chr1 135304596 135304597 +chr1 135346221 135346222 +chr1 135595351 135595352 +chr1 135645557 135645558 +chr1 135794196 135794197 +chr1 135833373 135833374 +chr1 136109219 136109220 +chr1 136151385 136151386 +chr1 136219228 136219229 +chr1 136276302 136276303 +chr1 136409892 136409893 +chr1 136846450 136846451 +chr1 137021089 137021090 +chr1 137057829 137057830 +chr1 137256872 137256873 +chr1 137292997 137292998 +chr1 137340715 137340716 +chr1 137563013 137563014 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148727077 148727078 +chr1 148900032 148900033 +chr1 148988309 148988310 +chr1 149151516 149151517 +chr1 149373423 149373424 +chr1 149547172 149547173 +chr1 149930099 149930100 +chr1 150523771 150523772 +chr1 151852781 151852782 +chr1 151941991 151941992 +chr1 152055844 152055845 +chr1 152768992 152768993 +chr1 153117376 153117377 +chr1 153562593 153562594 +chr1 153617551 153617552 +chr1 154259255 154259256 +chr1 154305193 154305194 +chr1 154793310 154793311 +chr1 154959021 154959022 +chr1 155608292 155608293 +chr1 155676641 155676642 +chr1 155882149 155882150 +chr1 156957961 156957962 +chr1 157054389 157054390 +chr1 157229460 157229461 +chr1 157232537 157232538 +chr1 157353367 157353368 +chr1 157530064 157530065 +chr1 157616665 157616666 +chr1 157708175 157708176 +chr1 157854160 157854161 +chr1 157916567 157916568 +chr1 157960555 157960556 +chr1 158166030 158166031 +chr1 158365460 158365461 +chr1 158890212 158890213 +chr1 159139993 159139994 +chr1 159875548 159875549 diff -r 000000000000 -r d9c1f2133124 test-data/mm9_summits.xls Binary file test-data/mm9_summits.xls has changed diff -r 000000000000 -r d9c1f2133124 test-data/mm9_summits_to_transcripts.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_summits_to_transcripts.out Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,10 @@ +#geneID chr_RNA start end strand differentially_expressed number_of_peaks chr_ChIP_1 summit_1 distance_1 +Xkr4 chr1 3204562 3661579 - None 1 chr1 3621547 40032 +AK149000 chr1 3638391 3648985 - None 1 chr1 3621547 27438 +Rp1 chr1 4333587 4350395 - None 0 --- --- --- +Sox17 chr1 4481008 4486494 - None 0 --- --- --- +Mrpl15 chr1 4763278 4775807 - None 0 --- --- --- +Lypla1 chr1 4797973 4836816 + None 0 --- --- --- +Tcea1 chr1 4847774 4887990 + None 0 --- --- --- +Rgs20 chr1 4899656 5060366 - None 0 --- --- --- +Atp6v1h chr1 5073253 5152630 + None 0 --- --- --- diff -r 000000000000 -r d9c1f2133124 test-data/mm9_transcripts_to_edges.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_transcripts_to_edges.out Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 3213477 3213513 Xkr4 - 3661579 3204562 8915 448066 8915 1 0 +chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 0 0 +chr1 3621547 3621583 Xkr4 - 3661579 3204562 39996 39996 416985 1 0 diff -r 000000000000 -r d9c1f2133124 test-data/mm9_transcripts_to_edges.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_transcripts_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,3 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 3213477 3213513 Xkr4 - 3661579 3204562 8915 448066 8915 1 0 +chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 0 0 diff -r 000000000000 -r d9c1f2133124 test-data/mm9_tss_to_edges.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_tss_to_edges.out Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,3 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 0 0 +chr1 3621547 3621583 Xkr4 - 3661579 3204562 39996 39996 416985 1 0 diff -r 000000000000 -r d9c1f2133124 test-data/mm9_tss_to_edges.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_tss_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,2 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 0 0 diff -r 000000000000 -r d9c1f2133124 test-data/mm9_tss_to_summits.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_tss_to_summits.out Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,504 @@ +#chr start geneID nearest TSS distance_to_TSS distance_to_TES strand in_the_gene transcripts_inbetween transcript_ids_inbetween +chr1 3213477 . . . . . . . . . +chr1 3542857 AK149000 1 of 2 3648985 106128 95534 - NO 0 +chr1 3542857 Xkr4 2 of 2 3661579 118722 -338295 - YES 1 AK149000 +chr1 3560979 AK149000 1 of 2 3648985 88006 77412 - NO 0 +chr1 3560979 Xkr4 2 of 2 3661579 100600 -356417 - YES 1 AK149000 +chr1 3621547 AK149000 1 of 2 3648985 27438 16844 - NO 0 +chr1 3621547 Xkr4 2 of 2 3661579 40032 -416985 - YES 1 AK149000 +chr1 4630453 . . . . . . . . . +chr1 5261737 . . . . . . . . . +chr1 5562257 . . . . . . . . . +chr1 6926999 . . . . . . . . . +chr1 7262846 . . . . . . . . . +chr1 7322487 . . . . . . . . . +chr1 7666187 . . . . . . . . . +chr1 7744070 . . . . . . . . . +chr1 7969291 . . . . . . . . . +chr1 8421057 . . . . . . . . . +chr1 8679021 . . . . . . . . . +chr1 9359611 . . . . . . . . . +chr1 9415439 . . . . . . . . . +chr1 9608130 . . . . . . . . . +chr1 9616803 . . . . . . . . . +chr1 9897397 . . . . . . . . . +chr1 10251725 . . . . . . . . . +chr1 10254195 . . . . . . . . . +chr1 10305254 . . . . . . . . . +chr1 10451286 . . . . . . . . . +chr1 11340573 . . . . . . . . . +chr1 11610483 . . . . . . . . . +chr1 11960381 . . . . . . . . . +chr1 11987310 . . . . . . . . . +chr1 12441678 . . . . . . . . . +chr1 12704380 . . . . . . . . . +chr1 12871650 . . . . . . . . . +chr1 13179280 . . . . . . . . . +chr1 13934524 . . . . . . . . . +chr1 14479277 . . . . . . . . . +chr1 14755996 . . . . . . . . . +chr1 14848637 . . . . . . . . . +chr1 14967919 . . . . . . . . . +chr1 15097029 . . . . . . . . . +chr1 17128114 . . . . . . . . . +chr1 17160496 . . . . . . . . . +chr1 17334281 . . . . . . . . . +chr1 17605285 . . . . . . . . . +chr1 17922903 . . . . . . . . . +chr1 18681561 . . . . . . . . . +chr1 19213304 . . . . . . . . . +chr1 20317581 . . . . . . . . . +chr1 21466434 . . . . . . . . . +chr1 22074908 . . . . . . . . . +chr1 22696516 . . . . . . . . . +chr1 23655828 . . . . . . . . . +chr1 24583893 . . . . . . . . . +chr1 24738828 . . . . . . . . . +chr1 24743796 . . . . . . . . . +chr1 25009857 . . . . . . . . . +chr1 25313509 . . . . . . . . . +chr1 26503310 . . . . . . . . . +chr1 27025916 . . . . . . . . . +chr1 27385857 . . . . . . . . . +chr1 27598627 . . . . . . . . . +chr1 27636264 . . . . . . . . . +chr1 27687524 . . . . . . . . . +chr1 28357424 . . . . . . . . . +chr1 29135026 . . . . . . . . . +chr1 29633575 . . . . . . . . . +chr1 29825940 . . . . . . . . . +chr1 30137793 . . . . . . . . . +chr1 30142141 . . . . . . . . . +chr1 30465754 . . . . . . . . . +chr1 30785908 . . . . . . . . . +chr1 31077695 . . . . . . . . . +chr1 31123645 . . . . . . . . . +chr1 31158742 . . . . . . . . . +chr1 31883682 . . . . . . . . . +chr1 31990075 . . . . . . . . . +chr1 33079863 . . . . . . . . . +chr1 33288587 . . . . . . . . . +chr1 33856089 . . . . . . . . . +chr1 34588477 . . . . . . . . . +chr1 34633149 . . . . . . . . . +chr1 34749000 . . . . . . . . . +chr1 34764419 . . . . . . . . . +chr1 35032286 . . . . . . . . . +chr1 35047073 . . . . . . . . . +chr1 35933401 . . . . . . . . . +chr1 36135485 . . . . . . . . . +chr1 36742521 . . . . . . . . . +chr1 36859752 . . . . . . . . . +chr1 37388614 . . . . . . . . . +chr1 37763263 . . . . . . . . . +chr1 37824535 . . . . . . . . . +chr1 37974386 . . . . . . . . . +chr1 37994576 . . . . . . . . . +chr1 38460553 . . . . . . . . . +chr1 38502464 . . . . . . . . . +chr1 38761349 . . . . . . . . . +chr1 38832604 . . . . . . . . . +chr1 39388554 . . . . . . . . . +chr1 39439044 . . . . . . . . . +chr1 39593773 . . . . . . . . . +chr1 39693273 . . . . . . . . . +chr1 39924300 . . . . . . . . . +chr1 40132160 . . . . . . . . . +chr1 40243823 . . . . . . . . . +chr1 40426457 . . . . . . . . . +chr1 40773529 . . . . . . . . . +chr1 40785687 . . . . . . . . . +chr1 40953366 . . . . . . . . . +chr1 41021129 . . . . . . . . . +chr1 41080072 . . . . . . . . . +chr1 41138125 . . . . . . . . . +chr1 41154639 . . . . . . . . . +chr1 42299563 . . . . . . . . . +chr1 42463569 . . . . . . . . . +chr1 42518766 . . . . . . . . . +chr1 43783219 . . . . . . . . . +chr1 44575305 . . . . . . . . . +chr1 44600563 . . . . . . . . . +chr1 44982842 . . . . . . . . . +chr1 45305515 . . . . . . . . . +chr1 45339758 . . . . . . . . . +chr1 45422086 . . . . . . . . . +chr1 45824016 . . . . . . . . . +chr1 46360753 . . . . . . . . . +chr1 46527798 . . . . . . . . . +chr1 47047692 . . . . . . . . . +chr1 48153542 . . . . . . . . . +chr1 48306038 . . . . . . . . . +chr1 48454759 . . . . . . . . . +chr1 49437523 . . . . . . . . . +chr1 49709489 . . . . . . . . . +chr1 50863175 . . . . . . . . . +chr1 50927909 . . . . . . . . . +chr1 51137708 . . . . . . . . . +chr1 51204752 . . . . . . . . . +chr1 51769267 . . . . . . . . . +chr1 52110888 . . . . . . . . . +chr1 52123042 . . . . . . . . . +chr1 52272863 . . . . . . . . . +chr1 52840700 . . . . . . . . . +chr1 52890780 . . . . . . . . . +chr1 53450997 . . . . . . . . . +chr1 53599262 . . . . . . . . . +chr1 53784753 . . . . . . . . . +chr1 53990993 . . . . . . . . . +chr1 54016877 . . . . . . . . . +chr1 54073194 . . . . . . . . . +chr1 54258499 . . . . . . . . . +chr1 54429617 . . . . . . . . . +chr1 54526981 . . . . . . . . . +chr1 54655149 . . . . . . . . . +chr1 55664918 . . . . . . . . . +chr1 55720320 . . . . . . . . . +chr1 55720320 . . . . . . . . . +chr1 56585857 . . . . . . . . . +chr1 56639054 . . . . . . . . . +chr1 56791957 . . . . . . . . . +chr1 57250654 . . . . . . . . . +chr1 57825391 . . . . . . . . . +chr1 58106272 . . . . . . . . . +chr1 58642339 . . . . . . . . . +chr1 58778630 . . . . . . . . . +chr1 59053239 . . . . . . . . . +chr1 59066499 . . . . . . . . . +chr1 59162431 . . . . . . . . . +chr1 59271155 . . . . . . . . . +chr1 59457887 . . . . . . . . . +chr1 59699258 . . . . . . . . . +chr1 59898050 . . . . . . . . . +chr1 60028370 . . . . . . . . . +chr1 60369879 . . . . . . . . . +chr1 60744666 . . . . . . . . . +chr1 61132096 . . . . . . . . . +chr1 61388934 . . . . . . . . . +chr1 62049483 . . . . . . . . . +chr1 62591289 . . . . . . . . . +chr1 62787008 . . . . . . . . . +chr1 62849190 . . . . . . . . . +chr1 63330804 . . . . . . . . . +chr1 63589255 . . . . . . . . . +chr1 63668100 . . . . . . . . . +chr1 63717943 . . . . . . . . . +chr1 64203406 . . . . . . . . . +chr1 65589476 . . . . . . . . . +chr1 66584321 . . . . . . . . . +chr1 66650744 . . . . . . . . . +chr1 66765432 . . . . . . . . . +chr1 66788077 . . . . . . . . . +chr1 68081964 . . . . . . . . . +chr1 68240850 . . . . . . . . . +chr1 68261167 . . . . . . . . . +chr1 68449665 . . . . . . . . . +chr1 68860261 . . . . . . . . . +chr1 69018088 . . . . . . . . . +chr1 69039525 . . . . . . . . . +chr1 69161322 . . . . . . . . . +chr1 69672941 . . . . . . . . . +chr1 69981290 . . . . . . . . . +chr1 70212174 . . . . . . . . . +chr1 70438453 . . . . . . . . . +chr1 71145915 . . . . . . . . . +chr1 71240778 . . . . . . . . . +chr1 72471214 . . . . . . . . . +chr1 72645850 . 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. . . +chr1 81263506 . . . . . . . . . +chr1 81379046 . . . . . . . . . +chr1 81819254 . . . . . . . . . +chr1 81947775 . . . . . . . . . +chr1 82250362 . . . . . . . . . +chr1 82413188 . . . . . . . . . +chr1 83247390 . . . . . . . . . +chr1 84040616 . . . . . . . . . +chr1 84092931 . . . . . . . . . +chr1 84344563 . . . . . . . . . +chr1 84408932 . . . . . . . . . +chr1 85094874 . . . . . . . . . +chr1 85528842 . . . . . . . . . +chr1 85826904 . . . . . . . . . +chr1 85964560 . . . . . . . . . +chr1 86054265 . . . . . . . . . +chr1 86056284 . . . . . . . . . +chr1 86224644 . . . . . . . . . +chr1 87208129 . . . . . . . . . +chr1 87444219 . . . . . . . . . +chr1 87668513 . . . . . . . . . +chr1 88031697 . . . . . . . . . +chr1 88349216 . . . . . . . . . +chr1 88726246 . . . . . . . . . +chr1 88906288 . . . . . . . . . +chr1 89124499 . . . . . . . . . +chr1 89314873 . . . . . . . . . +chr1 89518437 . . . . . . . . . +chr1 89592486 . . . . . . . . . +chr1 89794182 . . . . . . . . . +chr1 90334569 . . . . . . . . . +chr1 90336926 . . . . . . . . . +chr1 92478057 . . . . . . . . . +chr1 92675608 . . . . . . . . . +chr1 92954933 . . . . . . . . . +chr1 93201581 . . . . . . . . . +chr1 93270331 . . . . . . . . . +chr1 93777476 . . . . . . . . . +chr1 94397193 . . . . . . . . . +chr1 94579866 . . . . . . . . . +chr1 94844232 . . . . . . . . . +chr1 95086554 . . . . . . . . . +chr1 95862340 . . . . . . . . . +chr1 96049515 . . . . . . . . . +chr1 97113889 . . . . . . . . . +chr1 97282222 . . . . . . . . . +chr1 97328039 . . . . . . . . . +chr1 97463124 . . . . . . . . . +chr1 98120197 . . . . . . . . . +chr1 98196449 . . . . . . . . . +chr1 98292255 . . . . . . . . . +chr1 98601476 . . . . . . . . . +chr1 99285499 . . . . . . . . . +chr1 99733007 . . . . . . . . . +chr1 100072537 . . . . . . . . . +chr1 100467147 . . . . . . . . . +chr1 100579796 . . . . . . . . . +chr1 100774096 . . . . . . . . . +chr1 100858400 . . . . . . . . . +chr1 100867231 . . . . . . . . . +chr1 100901957 . . . . . . . . . +chr1 100984978 . . . . . . . . . +chr1 101092578 . . . . . . . . . +chr1 101333258 . . . . . . . . . +chr1 101534314 . . . . . . . . . +chr1 101634036 . . . . . . . . . +chr1 101810843 . . . . . . . . . +chr1 102278981 . . . . . . . . . +chr1 102948274 . . . . . . . . . +chr1 103030355 . . . . . . . . . +chr1 103317576 . . . . . . . . . +chr1 103365957 . . . . . . . . . +chr1 103876850 . . . . . . . . . +chr1 104567287 . . . . . . . . . +chr1 105328975 . . . . . . . . . +chr1 105425643 . . . . . . . . . +chr1 105466279 . . . . . . . . . +chr1 105466954 . . . . . . . . . +chr1 105622547 . . . . . . . . . +chr1 105737319 . . . . . . . . . +chr1 105848647 . . . . . . . . . +chr1 106462232 . . . . . . . . . +chr1 106946512 . . . . . . . . . +chr1 107689889 . . . . . . . . . +chr1 108450749 . . . . . . . . . +chr1 108577325 . . . . . . . . . +chr1 108825391 . . . . . . . . . +chr1 108975480 . . . . . . . . . +chr1 109014805 . . . . . . . . . +chr1 109756119 . . . . . . . . . +chr1 110142400 . . . . . . . . . +chr1 110400829 . . . . . . . . . +chr1 110843948 . . . . . . . . . +chr1 110896336 . . . . . . . . . +chr1 110926419 . . . . . . . . . +chr1 111467637 . . . . . . . . . +chr1 111528830 . . . . . . . . . +chr1 111952975 . . . . . . . . . +chr1 112015854 . . . . . . . . . +chr1 112221526 . . . . . . . . . +chr1 112393742 . . . . . . . . . +chr1 112688739 . . . . . . . . . +chr1 112754960 . . . . . . . . . +chr1 114014178 . . . . . . . . . +chr1 114129449 . . . . . . . . . +chr1 114279757 . . . . . . . . . +chr1 114489355 . . . . . . . . . +chr1 114947413 . . . . . . . . . +chr1 115559737 . . . . . . . . . +chr1 115788413 . . . . . . . . . +chr1 116265932 . . . . . . . . . +chr1 116349373 . . . . . . . . . +chr1 116496527 . . . . . . . . . +chr1 116732364 . . . . . . . . . +chr1 116788050 . . . . . . . . . +chr1 117105699 . . . . . . . . . +chr1 117651574 . . . . . . . . . +chr1 117666069 . . . . . . . . . +chr1 118378031 . . . . . . . . . +chr1 119053534 . . . . . . . . . +chr1 119113385 . . . . . . . . . +chr1 119174525 . . . . . . . . . +chr1 119503762 . . . . . . . . . +chr1 119527726 . . . . . . . . . +chr1 119948214 . . . . . . . . . +chr1 120267925 . . . . . . . . . +chr1 120380981 . . . . . . . . . +chr1 120465310 . . . . . . . . . +chr1 120797706 . . . . . . . . . +chr1 121041195 . . . . . . . . . +chr1 121094948 . . . . . . . . . +chr1 121167893 . . . . . . . . . +chr1 121340746 . . . . . . . . . +chr1 121587267 . . . . . . . . . +chr1 121681260 . . . . . . . . . +chr1 121816202 . . . . . . . . . +chr1 123026661 . . . . . . . . . +chr1 123170986 . . . . . . . . . +chr1 123685384 . . . . . . . . . +chr1 123835178 . . . . . . . . . +chr1 123920817 . . . . . . . . . +chr1 123949970 . . . . . . . . . +chr1 124461424 . . . . . . . . . +chr1 125400371 . . . . . . . . . +chr1 126171930 . . . . . . . . . +chr1 126179030 . . . . . . . . . +chr1 126687579 . . . . . . . . . +chr1 126712327 . . . . . . . . . +chr1 126783497 . . . . . . . . . +chr1 126787012 . . . . . . . . . +chr1 126963082 . . . . . . . . . +chr1 127190153 . . . . . . . . . +chr1 127228396 . . . . . . . . . +chr1 127507342 . . . . . . . . . +chr1 127703188 . . . . . . . . . +chr1 127735504 . . . . . . . . . +chr1 128049231 . . . . . . . . . +chr1 128388917 . . . . . . . . . +chr1 128791747 . . . . . . . . . +chr1 129571914 . . . . . . . . . +chr1 129582844 . . . . . . . . . +chr1 130923911 . . . . . . . . . +chr1 131245002 . . . . . . . . . +chr1 131624212 . . . . . . . . . +chr1 131653028 . . . . . . . . . +chr1 131673494 . . . . . . . . . +chr1 131762457 . . . . . . . . . +chr1 132812150 . . . . . . . . . +chr1 133122490 . . . . . . . . . +chr1 133337646 . . . . . . . . . +chr1 134107973 . . . . . . . . . +chr1 134516117 . . . . . . . . . +chr1 134650852 . . . . . . . . . +chr1 135304596 . . . . . . . . . +chr1 135346221 . . . . . . . . . +chr1 135595351 . . . . . . . . . +chr1 135645557 . . . . . . . . . +chr1 135794196 . . . . . . . . . +chr1 135833373 . . . . . . . . . +chr1 136109219 . . . . . . . . . +chr1 136151385 . . . . . . . . . +chr1 136219228 . . . . . . . . . +chr1 136276302 . . . . . . . . . +chr1 136409892 . . . . . . . . . +chr1 136846450 . . . . . . . . . +chr1 137021089 . . . . . . . . . +chr1 137057829 . . . . . . . . . +chr1 137256872 . . . . . . . . . +chr1 137292997 . . . . . . . . . +chr1 137340715 . . . . . . . . . +chr1 137563013 . . . . . . . . . +chr1 138237818 . . . . . . . . . +chr1 138288739 . . . . . . . . . +chr1 138701415 . . . . . . . . . +chr1 138883160 . . . . . . . . . +chr1 139093105 . . . . . . . . . +chr1 139286502 . . . . . . . . . +chr1 139448680 . . . . . . . . . +chr1 139944056 . . . . . . . . . +chr1 140207040 . . . . . . . . . +chr1 141517452 . . . . . . . . . +chr1 142087663 . . . . . . . . . +chr1 142561476 . . . . . . . . . +chr1 142732555 . . . . . . . . . +chr1 142765329 . . . . . . . . . +chr1 142811575 . . . . . . . . . +chr1 142823331 . . . . . . . . . +chr1 142985887 . . . . . . . . . +chr1 143071919 . . . . . . . . . +chr1 143137676 . . . . . . . . . +chr1 143684082 . . . . . . . . . +chr1 143803869 . . . . . . . . . +chr1 143866547 . . . . . . . . . +chr1 144585588 . . . . . . . . . +chr1 145018626 . . . . . . . . . +chr1 145169340 . . . . . . . . . +chr1 145286043 . . . . . . . . . +chr1 145743816 . . . . . . . . . +chr1 145793073 . . . . . . . . . +chr1 145943835 . . . . . . . . . +chr1 145973347 . . . . . . . . . +chr1 146233793 . . . . . . . . . +chr1 146349912 . . . . . . . . . +chr1 146992848 . . . . . . . . . +chr1 147015972 . . . . . . . . . +chr1 147919367 . . . . . . . . . +chr1 148073000 . . . . . . . . . +chr1 148184896 . . . . . . . . . +chr1 148571263 . . . . . . . . . +chr1 148727077 . . . . . . . . . +chr1 148900032 . . . . . . . . . +chr1 148988309 . . . . . . . . . +chr1 149151516 . . . . . . . . . +chr1 149373423 . . . . . . . . . +chr1 149547172 . . . . . . . . . +chr1 149930099 . . . . . . . . . +chr1 150523771 . . . . . . . . . +chr1 151852781 . . . . . . . . . +chr1 151941991 . . . . . . . . . +chr1 152055844 . . . . . . . . . +chr1 152768992 . . . . . . . . . +chr1 153117376 . . . . . . . . . +chr1 153562593 . . . . . . . . . +chr1 153617551 . . . . . . . . . +chr1 154259255 . . . . . . . . . +chr1 154305193 . . . . . . . . . +chr1 154793310 . . . . . . . . . +chr1 154959021 . . . . . . . . . +chr1 155608292 . . . . . . . . . +chr1 155676641 . . . . . . . . . +chr1 155882149 . . . . . . . . . +chr1 156957961 . . . . . . . . . +chr1 157054389 . . . . . . . . . +chr1 157229460 . . . . . . . . . +chr1 157232537 . . . . . . . . . +chr1 157353367 . . . . . . . . . +chr1 157530064 . . . . . . . . . +chr1 157616665 . . . . . . . . . +chr1 157708175 . . . . . . . . . +chr1 157854160 . . . . . . . . . +chr1 157916567 . . . . . . . . . +chr1 157960555 . . . . . . . . . +chr1 158166030 . . . . . . . . . +chr1 158365460 . . . . . . . . . +chr1 158890212 . . . . . . . . . +chr1 159139993 . . . . . . . . . +chr1 159875548 . . . . . . . . . diff -r 000000000000 -r d9c1f2133124 test-data/peaks.xls Binary file test-data/peaks.xls has changed diff -r 000000000000 -r d9c1f2133124 test-data/peaks_to_transcripts.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks_to_transcripts.out Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,957 @@ +#geneID chr_RNA start end strand differentially_expressed number_of_peaks +AF064749_Col6a3 chr1 92566771 92800755 - 1 0 +AK015559_4930472D16Rik chr1 25020851 25021989 - 1 0 +AK030377_A330023F24Rik chr1 196781953 196826186 - 1 0 +AK080193_A530079E22Rik chr1 89401837 89403491 - 1 0 +AK082264_C230030N03Rik chr1 34735043 34781084 + 1 0 +BC006931_AI597479 chr1 43153807 43172843 + 1 0 +BC021773_Glb1l chr1 75193364 75207353 - 1 0 +BC023951_D1Ertd622e chr1 99540054 99558631 - 1 0 +BC028767_3110009E18Rik chr1 122017764 122114603 + 1 0 +BC031781_BC031781 chr1 182781250 182798240 + 1 0 +BC034187_BC035947 chr1 78493611 78497758 - 1 0 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101934704 102382815 + 0 0 +NM_172852_Serpinb13 chr1 108877561 108897772 + 0 0 +NM_172853_Cdh7 chr1 111718165 112036714 + 0 0 +NM_172974_Cops7b chr1 88478926 88503950 + 0 0 +NM_173029_Adcy10 chr1 167415324 167506904 + 0 0 +NM_173187_2310035C23Rik chr1 107560448 107651751 + 0 0 +NM_173378_Trp53bp2 chr1 184333536 184392728 + 0 0 +NM_173395_Fam132b chr1 93263007 93270794 + 0 0 +NM_173424_Zbtb37 chr1 162938038 162965197 - 0 0 +NM_173425_Fam124b chr1 80156958 80214611 - 0 0 +NM_173437_Nav1 chr1 137332309 137482282 - 0 0 +NM_173437_Nav1 chr1 137481360 137496527 + 0 0 +NM_173443_Vcpip1 chr1 9709587 9764569 - 0 0 +NM_173760_Hisppd1 chr1 99592475 99667685 - 0 0 +NM_173771_4933406M09Rik chr1 136282517 136287560 + 0 0 +NM_173772_Neu4 chr1 95917070 95928707 + 0 0 +NM_173865_Slc41a1 chr1 133724090 133745438 + 0 0 +NM_173868_St18 chr1 6477297 6885001 + 0 0 +NM_173870_Mgat4a chr1 37496234 37609425 - 0 0 +NM_174874_Atg4b chr1 95648097 95687167 + 0 0 +NM_174985_Gpbar1 chr1 74321873 74326272 + 0 0 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165245859 - 0 0 +NM_176916_Pld5 chr1 177892457 178205403 - 0 0 +NM_176972_Usp37 chr1 74482084 74590860 - 0 0 +NM_176980_Ankar chr1 72689581 72747143 - 0 0 +NM_177068_Olfml2b chr1 172569075 172612915 + 0 0 +NM_177084_Slc9a4 chr1 40636956 40687551 + 0 0 +NM_177129_Cntn2 chr1 134406005 134442705 - 0 0 +NM_177164_A830006F12Rik chr1 70772309 70929065 + 0 0 +NM_177173_A830018L16Rik chr1 11404178 11994163 + 0 0 +NM_177235_Bend6 chr1 33903283 33964764 - 0 0 +NM_177243_Slc26a9 chr1 133640599 133668075 + 0 0 +NM_177305_Arl4c chr1 90569702 90617572 - 0 0 +NM_177397_Atp6v1g3 chr1 140120875 140186039 + 0 0 +NM_177445_Dars chr1 130260284 130314013 - 0 0 +NM_177587_Aqp12 chr1 94886487 94908846 + 0 0 +NM_177604_AA986860 chr1 132628563 132644539 + 0 0 +NM_177643_Zfp281 chr1 138487073 138526617 + 0 0 +NM_177646_Dgkd chr1 89749836 89841946 + 0 0 +NM_177722_6030422M02Rik chr1 9898713 9932156 + 0 0 +NM_177723_Vsig8 chr1 174486069 174513273 + 0 0 +NM_177724_D230039L06Rik chr1 180426979 180686112 + 0 0 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132618643 + 0 0 +NM_178692_C130074G19Rik chr1 186695805 186707077 - 0 0 +NM_178775_Rps6kc1 chr1 192524091 192736016 - 0 0 +NM_178779_Rnf152 chr1 107176426 107253513 - 0 0 +NM_178874_Tmcc2 chr1 134252895 134288369 - 0 0 +NM_178883_Gorab chr1 165315039 165340946 - 0 0 +NM_178884_Obsl1 chr1 75482401 75503218 - 0 0 +NM_181405_Rnpepl1 chr1 94807467 94817954 + 0 0 +NM_181546_Syt14 chr1 194713536 194861959 - 0 0 +NM_181750_R3hdm1 chr1 129999892 130134312 + 0 0 +NM_181796_Gstp2 chr1 193897651 193905509 - 0 0 +NM_182716_Nfasc chr1 134445291 134638354 - 0 0 +NM_182930_Plekha6 chr1 135077806 135200008 + 0 0 +NM_183019_Arhgef4 chr1 34788954 34873560 + 0 0 +NM_183022_Accn4 chr1 75447063 75470207 + 0 0 +NM_183027_Ap1s3 chr1 79591820 79668545 - 0 0 +NM_183028_Pcmtd1 chr1 7079053 7163709 + 0 0 +NM_183124_Defb41 chr1 18241071 18350659 - 0 0 +NM_183355_Pbx1 chr1 170049495 170512777 - 0 0 +NM_183391_Tnfsf18 chr1 163373523 163524094 + 0 0 +NM_194333_Slc23a3 chr1 75120731 75130464 - 0 0 +NM_198006_6330578E17Rik chr1 37473934 37474944 - 0 0 +NM_198006_6330578E17Rik chr1 37477057 37486928 - 0 0 +NM_198028_Serpinb10 chr1 109425580 109445838 + 0 0 +NM_198127_Abi2 chr1 60466022 60537998 + 0 0 +NM_198247_Sertad4 chr1 194670313 194693726 - 0 0 +NM_198303_Eif5b chr1 38054627 38112414 + 0 0 +NM_198652_6430706D22Rik chr1 90158880 90174174 - 0 0 +NM_198653_Iars2 chr1 187109458 187153280 - 0 0 +NM_198654_Nsl1 chr1 192886918 192919389 + 0 0 +NM_198680_Serpinb3b chr1 109033488 109059720 - 0 0 +NM_198899_Ugcgl1 chr1 36196873 36301555 - 0 0 +NM_198934_Pou2f1 chr1 167804181 167932753 - 0 0 +NM_199007_Sgol2 chr1 58026657 58085164 + 0 0 +NM_199021_Dpp10 chr1 125044486 126749525 - 0 0 +NM_201363_Serpinb3c chr1 109088051 109198931 - 0 0 +NM_201376_Serpinb3d chr1 108974770 108980057 - 0 0 +NM_201641_Ugt1a10 chr1 89922380 90115570 + 0 0 +NM_206896_Olfr12 chr1 94516341 94538591 + 0 0 +NM_207031_Ano7 chr1 95270385 95302271 + 0 0 +NM_207137_Olfr417 chr1 176299050 176299979 + 0 0 +NM_207137_Olfr417 chr1 176321202 176322113 + 0 0 +NM_207158_Olfr427 chr1 176028781 176030538 + 0 0 +NM_207225_Hdac4 chr1 93755950 94103099 - 0 0 +NM_207228_Tsga10 chr1 37783457 37922148 - 0 0 +NM_207233_C1ql2 chr1 122196386 122239751 + 0 0 +NM_207281_4832428D23Rik chr1 44260915 44515719 - 0 0 +NM_207583_Fam5b chr1 160175402 160286644 - 0 0 +NM_207653_Cflar chr1 58768296 58813658 + 0 0 +NM_207653_Cflar chr1 58813703 58815725 + 0 0 +NM_213616_Atp2b4 chr1 135602265 135697538 - 0 0 +NR_002840_Gas5 chr1 162964758 162968663 + 0 0 +NR_002858_EG241041 chr1 21268965 21306401 - 0 0 +NR_002870_Dnm3os chr1 164119785 164155671 + 0 0 +NR_003623_EG277333 chr1 182251970 182262902 - 0 0 +NR_026896_4931440L10Rik chr1 136437533 136449760 - 0 0 diff -r 000000000000 -r d9c1f2133124 test-data/rnachipintegrator_canonical_genes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnachipintegrator_canonical_genes.loc Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,1 @@ +mm9_test mm9 mm9 ${__HERE__}/mm9_canonical_genes.tsv diff -r 000000000000 -r d9c1f2133124 test-data/summits.xls Binary file test-data/summits.xls has changed diff -r 000000000000 -r d9c1f2133124 test-data/transcripts_to_edges.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_to_edges.out Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 0 0 +chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 0 0 +chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 0 0 diff -r 000000000000 -r d9c1f2133124 test-data/transcripts_to_edges.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 0 0 +chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 0 0 +chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 0 0 diff -r 000000000000 -r d9c1f2133124 test-data/tss_to_edges.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_to_edges.out Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 0 0 +chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 0 0 +chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 0 0 diff -r 000000000000 -r d9c1f2133124 test-data/tss_to_edges.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,4 @@ +#chr start end geneID strand TSS TES dist_closest_edge dist_TSS dist_TES overlap_transcript overlap_promoter +chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 0 0 +chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 0 0 +chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 0 0 diff -r 000000000000 -r d9c1f2133124 test-data/tss_to_summits.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tss_to_summits.out Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,654 @@ +#chr start geneID nearest TSS distance_to_TSS distance_to_TES strand in_the_gene transcripts_inbetween transcript_ids_inbetween +chr10 106033584 . . . . . . . . . +chr10 106033751 . . . . . . . . . +chr10 107429926 . . . . . . . . . +chr10 114752719 . . . . . . . . . +chr10 114994096 . . . . . . . . . +chr10 127058840 . . . . . . . . . +chr10 127184557 . . . . . . . . . +chr10 13089536 . . . . . . . . . +chr10 13408622 . . . . . . . . . +chr10 17725474 . . . . . . . . . +chr10 21862583 . . . . . . . . . +chr10 21862774 . . . . . . . . . +chr10 31587625 . . . . . . . . . +chr10 41613298 . . . . . . . . . +chr10 43640892 . . . . . . . . . +chr10 43740181 . . . . . . . . . +chr10 45093322 . . . . . . . . . +chr10 57702300 . . . . . . . . . +chr10 59362596 . . . . . . . . . +chr10 59693654 . . . . . . . . . +chr10 60613588 . . . . . . . . . +chr10 60696228 . . . . . . . . . +chr10 67567003 . . . . . . . . . +chr10 76664902 . . . . . . . . . +chr10 7707698 . . . . . . . . . +chr10 79808095 . . . . . . . . . +chr10 80126390 . . . . . . . . . +chr10 81033719 . . . . . . . . . +chr10 82306942 . . . . . . . . . +chr10 82517145 . . . . . . . . . +chr10 84922053 . . . . . . . . . +chr10 88433836 . . . . . . . . . +chr10 89195191 . . . . . . . . . +chr10 93642365 . . . . . . . . . +chr10 94183365 . . . . . . . . . +chr10 94306306 . . . . . . . . . +chr1 10627335 . . . . . . . . . +chr1 108757655 . . . . . . . . . +chr11 100148455 . . . . . . . . . +chr11 100964551 . . . . . . . . . +chr11 102973374 . . . . . . . . . +chr11 103196320 . . . . . . . . . +chr11 107278688 . . . . . . . . . +chr11 110241161 . . . . . . . . . +chr11 114563829 . . . . . . . . . +chr11 115639021 . . . . . . . . . +chr11 115836265 . . . . . . . . . +chr11 119827740 . . . . . . . . . +chr11 120952392 . . . . . . . . . +chr11 121341339 . . . . . . . . . +chr11 16560450 . . . . . . . . . +chr11 18798190 . . . . . . . . . +chr11 19003164 . . . . . . . . . +chr11 20247624 . . . . . . . . . +chr1 120770337 . . . . . . . . . +chr11 21483462 . . . . . . . . . +chr11 29514477 . . . . . . . . . +chr11 3000481 . . . . . . . . . +chr11 3266659 . . . . . . . . . +chr1 132961088 . . . . . . . . . +chr1 133124938 . . . . . . . . . +chr11 34495361 . . . . . . . . . +chr1 135592753 . . . . . . . . . +chr1 135862036 . . . . . . . . . +chr1 136966533 . . . . . . . . . +chr1 13839396 . . . . . . . . . +chr1 138447793 . . . . . . . . . +chr1 140391721 . . . . . . . . . +chr11 4116866 . . . . . . . . . +chr1 145601109 . . . . . . . . . +chr11 50300699 . . . . . . . . . +chr11 5481053 . . . . . . . . . +chr1 154981623 . . . . . . . . . +chr1 155133374 . . . . . . . . . +chr1 158520668 . . . . . . . . . +chr1 158547339 . . . . . . . . . +chr1 158590699 . . . . . . . . . +chr1 158845321 . . . . . . . . . +chr1 159250801 BC055845_2810025M15Rik 1 of 1 159342483 91682 99552 + NO 0 +chr11 59272503 . . . . . . . . . +chr11 6069204 . . . . . . . . . +chr1 163837980 . . . . . . . . . +chr1 164225779 . . . . . . . . . +chr1 167233113 . . . . . . . . . +chr1 167916419 . . . . . . . . . +chr11 69572437 . . . . . . . . . +chr1 170265171 . . . . . . . . . +chr11 70397406 . . . . . . . . . +chr1 17040475 . . . . . . . . . +chr1 172630846 . . . . . . . . . +chr1 172630999 . . . . . . . . . +chr1 174386565 . . . . . . . . . +chr11 76126479 . . . . . . . . . +chr1 181071373 . . . . . . . . . +chr1 182489776 . . . . . . . . . +chr11 83860977 . . . . . . . . . +chr11 84381942 . . . . . . . . . +chr11 8483612 . . . . . . . . . +chr11 8541945 . . . . . . . . . +chr1 185865026 . . . . . . . . . +chr11 87257043 . . . . . . . . . +chr11 87967409 . . . . . . . . . +chr11 87967599 . . . . . . . . . +chr11 93986729 . . . . . . . . . +chr1 194268840 . . . . . . . . . +chr1 194655297 . . . . . . . . . +chr1 194967560 BC055955_A130010J15Rik 1 of 1 194999663 32103 36455 + NO 1 NM_016851_Irf6 +chr1 195334592 . . . . . . . . . +chr1 195340816 . . . . . . . . . +chr1 195348466 . . . . . . . . . +chr1 195352857 . . . . . . . . . +chr1 195394981 . . . . . . . . . +chr1 197067820 . . . . . . . . . +chr11 97171690 . . . . . . . . . +chr11 97233548 . . . . . . . . . +chr11 97297212 . . . . . . . . . +chr12 104299157 . . . . . . . . . +chr12 106237696 . . . . . . . . . +chr12 106674392 . . . . . . . . . +chr12 112330425 . . . . . . . . . +chr12 112477144 . . . . . . . . . +chr12 112975712 . . . . . . . . . +chr12 113981451 . . . . . . . . . +chr12 114119343 . . . . . . . . . +chr12 117853390 . . . . . . . . . +chr12 25562241 . . . . . . . . . +chr12 25648378 . . . . . . . . . +chr12 37211753 . . . . . . . . . +chr1 24619593 . . . . . . . . . +chr1 24619958 . . . . . . . . . +chr1 24741037 . . . . . . . . . +chr12 57923295 . . . . . . . . . +chr12 58725309 . . . . . . . . . +chr1 26744340 . . . . . . . . . +chr12 70755181 . . . . . . . . . +chr12 72971895 . . . . . . . . . +chr12 80608252 . . . . . . . . . +chr12 86926811 . . . . . . . . . +chr12 92932316 . . . . . . . . . +chr12 92984595 . . . . . . . . . +chr13 10082361 . . . . . . . . . +chr13 102618599 . . . . . . . . . +chr13 103679464 . . . . . . . . . +chr13 104768206 . . . . . . . . . +chr13 110051416 . . . . . . . . . +chr13 113548696 . . . . . . . . . +chr13 120276594 . . . . . . . . . +chr13 12578010 . . . . . . . . . +chr13 23610160 . . . . . . . . . +chr13 33170306 . . . . . . . . . +chr13 38172741 . . . . . . . . . +chr13 38254769 . . . . . . . . . +chr13 40820500 . . . . . . . . . +chr1 34217012 . . . . . . . . . +chr13 47047075 . . . . . . . . . +chr13 47062921 . . . . . . . . . +chr13 56003795 . . . . . . . . . +chr13 57960273 . . . . . . . . . +chr1 36116936 . . . . . . . . . +chr13 63189880 . . . . . . . . . +chr13 63381834 . . . . . . . . . +chr13 73643112 . . . . . . . . . +chr13 91318240 . . . . . . . . . +chr13 91510502 . . . . . . . . . +chr1 39502327 BC049091_D1Bwg0212e 1 of 1 39592545 90218 101407 + NO 1 NM_018775_Tbc1d8 +chr13 96258876 . . . . . . . . . +chr13 97344282 . . . . . . . . . +chr13 98808966 . . . . . . . . . +chr1 40336020 . . . . . . . . . +chr14 11823985 . . . . . . . . . +chr14 120603083 . . . . . . . . . +chr14 120721569 . . . . . . . . . +chr14 21906019 . . . . . . . . . +chr14 26296311 . . . . . . . . . +chr14 33150022 . . . . . . . . . +chr14 41762023 . . . . . . . . . +chr1 44205544 . . . . . . . . . +chr14 48866037 . . . . . . . . . +chr14 51711605 . . . . . . . . . +chr14 52550650 . . . . . . . . . +chr14 55194787 . . . . . . . . . +chr14 57316903 . . . . . . . . . +chr14 58540770 . . . . . . . . . +chr14 61693994 . . . . . . . . . +chr14 61973511 . . . . . . . . . +chr14 63456124 . . . . . . . . . +chr14 65935630 . . . . . . . . . +chr14 69265002 . . . . . . . . . +chr14 69273108 . . . . . . . . . +chr14 70724643 . . . . . . . . . +chr14 73637753 . . . . . . . . . +chr14 73655550 . . . . . . . . . +chr14 73713362 . . . . . . . . . +chr14 73770668 . . . . . . . . . +chr14 75184388 . . . . . . . . . +chr14 75346569 . . . . . . . . . +chr14 76292024 . . . . . . . . . +chr14 79927582 . . . . . . . . . +chr14 9521198 . . . . . . . . . +chr15 100992242 . . . . . . . . . +chr15 101063407 . . . . . . . . . +chr15 101563471 . . . . . . . . . +chr15 102066010 . . . . . . . . . +chr1 52635488 . . . . . . . . . +chr15 32250651 . . . . . . . . . +chr15 35249192 . . . . . . . . . +chr15 35631086 . . . . . . . . . +chr15 37127869 . . . . . . . . . +chr1 54641754 . . . . . . . . . +chr1 55293624 . . . . . . . . . +chr15 53027764 . . . . . . . . . +chr15 53130961 . . . . . . . . . +chr15 54185561 . . . . . . . . . +chr15 55202036 . . . . . . . . . +chr15 57480129 . . . . . . . . . +chr15 74917152 . . . . . . . . . +chr15 74917383 . . . . . . . . . +chr15 75989308 . . . . . . . . . +chr15 77629316 . . . . . . . . . +chr15 77661605 . . . . . . . . . +chr15 80038823 . . . . . . . . . +chr15 80533396 . . . . . . . . . +chr15 80691860 . . . . . . . . . +chr15 82973449 . . . . . . . . . +chr15 84022595 . . . . . . . . . +chr15 85064373 . . . . . . . . . +chr15 97706407 . . . . . . . . . +chr15 99628562 . . . . . . . . . +chr16 16866444 . . . . . . . . . +chr16 16912317 . . . . . . . . . +chr16 17866100 . . . . . . . . . +chr16 17949763 . . . . . . . . . +chr16 24948588 . . . . . . . . . +chr16 25385707 . . . . . . . . . +chr16 25836029 . . . . . . . . . +chr16 25843933 . . . . . . . . . +chr16 31290592 . . . . . . . . . +chr16 33883661 . . . . . . . . . +chr16 34430325 . . . . . . . . . +chr16 35981824 . . . . . . . . . +chr1 63674953 . . . . . . . . . +chr16 43508591 . . . . . . . . . +chr16 43574371 . . . . . . . . . +chr16 44101459 . . . . . . . . . +chr16 57391635 . . . . . . . . . +chr16 57391748 . . . . . . . . . +chr16 62799541 . . . . . . . . . +chr16 6295331 . . . . . . . . . +chr16 70314810 . . . . . . . . . +chr16 72688706 . . . . . . . . . +chr16 78632436 . . . . . . . . . +chr16 90095387 . . . . . . . . . +chr16 90151215 . . . . . . . . . +chr16 90468446 . . . . . . . . . +chr16 91875996 . . . . . . . . . +chr16 92744754 . . . . . . . . . +chr16 94024219 . . . . . . . . . +chr16 94427408 . . . . . . . . . +chr16 95881212 . . . . . . . . . +chr16 96224521 . . . . . . . . . +chr17 17959961 . . . . . . . . . +chr17 23681171 . . . . . . . . . +chr1 72779940 . . . . . . . . . +chr1 72780142 . . . . . . . . . +chr1 72825630 . . . . . . . . . +chr17 28478172 . . . . . . . . . +chr17 28834572 . . . . . . . . . +chr17 31823497 . . . . . . . . . +chr17 31979297 . . . . . . . . . +chr17 33920556 . . . . . . . . . +chr17 36368235 . . . . . . . . . +chr17 39981683 . . . . . . . . . +chr17 39985109 . . . . . . . . . +chr17 43064430 . . . . . . . . . +chr17 45715395 . . . . . . . . . +chr17 46403243 . . . . . . . . . +chr17 46403380 . . . . . . . . . +chr17 47404360 . . . . . . . . . +chr1 75491987 . . . . . . . . . +chr17 56447632 . . . . . . . . . +chr17 71508749 . . . . . . . . . +chr1 77467717 . . . . . . . . . +chr17 78655126 . . . . . . . . . +chr17 79794315 . . . . . . . . . +chr17 84737002 . . . . . . . . . +chr1 78641027 . . . . . . . . . +chr18 11755885 . . . . . . . . . +chr18 12671183 . . . . . . . . . +chr18 34147214 . . . . . . . . . +chr18 35061192 . . . . . . . . . +chr18 39723442 . . . . . . . . . +chr18 40467892 . . . . . . . . . +chr18 42207995 . . . . . . . . . +chr18 42930957 . . . . . . . . . +chr18 43135643 . . . . . . . . . +chr18 43419069 . . . . . . . . . +chr18 43419219 . . . . . . . . . +chr18 44675226 . . . . . . . . . +chr18 47529528 . . . . . . . . . +chr18 5016849 . . . . . . . . . +chr18 50224778 . . . . . . . . . +chr18 57946142 . . . . . . . . . +chr18 61428548 . . . . . . . . . +chr18 61934208 . . . . . . . . . +chr18 65457025 . . . . . . . . . +chr1 88419118 . . . . . . . . . +chr18 9428997 . . . . . . . . . +chr1 89999634 . . . . . . . . . +chr1 90423032 . . . . . . . . . +chr1 90602564 . . . . . . . . . +chr19 10798384 . . . . . . . . . +chr1 91506074 . . . . . . . . . +chr1 91506237 . . . . . . . . . +chr1 92080342 . . . . . . . . . +chr19 26820923 . . . . . . . . . +chr19 47782532 . . . . . . . . . +chr1 95196573 . . . . . . . . . +chr19 53969373 . . . . . . . . . +chr19 5846865 . . . . . . . . . +chr19 61275648 . . . . . . . . . +chr1 9629107 . . . . . . . . . +chr1 9629279 . . . . . . . . . +chr19 9018714 . . . . . . . . . +chr19 9062346 . . . . . . . . . +chr19 9144947 . . . . . . . . . +chr2 102274223 . . . . . . . . . +chr2 102288220 . . . . . . . . . +chr2 104540072 . . . . . . . . . +chr2 109810219 . . . . . . . . . +chr2 110568326 . . . . . . . . . +chr2 112043286 . . . . . . . . . +chr2 122171434 . . . . . . . . . +chr2 126962808 . . . . . . . . . +chr2 127332233 . . . . . . . . . +chr2 129432150 . . . . . . . . . +chr2 130201294 . . . . . . . . . +chr2 131923486 . . . . . . . . . +chr2 132577421 . . . . . . . . . +chr2 136745391 . . . . . . . . . +chr2 13696935 . . . . . . . . . +chr2 140652077 . . . . . . . . . +chr2 146397541 . . . . . . . . . +chr2 148295584 . . . . . . . . . +chr2 148343818 . . . . . . . . . +chr2 148558303 . . . . . . . . . +chr2 157260393 . . . . . . . . . +chr2 160572977 . . . . . . . . . +chr2 164682813 . . . . . . . . . +chr2 165427405 . . . . . . . . . +chr2 165720222 . . . . . . . . . +chr2 168745748 . . . . . . . . . +chr2 172759694 . . . . . . . . . +chr2 172763360 . . . . . . . . . +chr2 173901730 . . . . . . . . . +chr2 25988548 . . . . . . . . . +chr2 27585569 . . . . . . . . . +chr2 28282918 . . . . . . . . . +chr2 30663471 . . . . . . . . . +chr2 31019531 . . . . . . . . . +chr2 31119743 . . . . . . . . . +chr2 35346371 . . . . . . . . . +chr2 35518012 . . . . . . . . . +chr2 35524862 . . . . . . . . . +chr2 38355143 . . . . . . . . . +chr2 38843815 . . . . . . . . . +chr2 38843972 . . . . . . . . . +chr2 52035090 . . . . . . . . . +chr2 5300381 . . . . . . . . . +chr2 59285910 . . . . . . . . . +chr2 60283369 . . . . . . . . . +chr2 65385479 . . . . . . . . . +chr2 68763818 . . . . . . . . . +chr2 76386556 . . . . . . . . . +chr3 100835953 . . . . . . . . . +chr3 101743281 . . . . . . . . . +chr3 10277579 . . . . . . . . . +chr3 108226998 . . . . . . . . . +chr3 109489624 . . . . . . . . . +chr3 109687117 . . . . . . . . . +chr3 115822204 . . . . . . . . . +chr3 116529685 . . . . . . . . . +chr3 121601368 . . . . . . . . . +chr3 122624125 . . . . . . . . . +chr3 131236567 . . . . . . . . . +chr3 133263978 . . . . . . . . . +chr3 133271907 . . . . . . . . . +chr3 148641587 . . . . . . . . . +chr3 148641735 . . . . . . . . . +chr3 151026490 . . . . . . . . . +chr3 151774393 . . . . . . . . . +chr3 159510847 . . . . . . . . . +chr3 27907564 . . . . . . . . . +chr3 29852588 . . . . . . . . . +chr3 30992357 . . . . . . . . . +chr3 37395368 . . . . . . . . . +chr3 52130683 . . . . . . . . . +chr3 52912682 . . . . . . . . . +chr3 53475904 . . . . . . . . . +chr3 59001668 . . . . . . . . . +chr3 60421600 . . . . . . . . . +chr3 60421744 . . . . . . . . . +chr3 67769446 . . . . . . . . . +chr3 69758259 . . . . . . . . . +chr3 7487953 . . . . . . . . . +chr3 79711488 . . . . . . . . . +chr3 80988962 . . . . . . . . . +chr3 83579412 . . . . . . . . . +chr3 83791586 . . . . . . . . . +chr3 83863238 . . . . . . . . . +chr3 85735976 . . . . . . . . . +chr3 87369620 . . . . . . . . . +chr3 88458239 . . . . . . . . . +chr3 90049693 . . . . . . . . . +chr3 92698059 . . . . . . . . . +chr3 96066220 . . . . . . . . . +chr4 100623172 . . . . . . . . . +chr4 105979770 . . . . . . . . . +chr4 116862731 . . . . . . . . . +chr4 117295856 . . . . . . . . . +chr4 118220858 . . . . . . . . . +chr4 122723762 . . . . . . . . . +chr4 123266401 . . . . . . . . . +chr4 126168413 . . . . . . . . . +chr4 129093950 . . . . . . . . . +chr4 129413697 . . . . . . . . . +chr4 132011663 . . . . . . . . . +chr4 133155902 . . . . . . . . . +chr4 133160955 . . . . . . . . . +chr4 135129138 . . . . . . . . . +chr4 136010879 . . . . . . . . . +chr4 136838756 . . . . . . . . . +chr4 137004194 . . . . . . . . . +chr4 140731847 . . . . . . . . . +chr4 141160758 . . . . . . . . . +chr4 141297891 . . . . . . . . . +chr4 144482189 . . . . . . . . . +chr4 150245511 . . . . . . . . . +chr4 151779151 . . . . . . . . . +chr4 151779297 . . . . . . . . . +chr4 153446235 . . . . . . . . . +chr4 155148830 . . . . . . . . . +chr4 155164911 . . . . . . . . . +chr4 35037416 . . . . . . . . . +chr4 40845966 . . . . . . . . . +chr4 41654489 . . . . . . . . . +chr4 45434915 . . . . . . . . . +chr4 53231170 . . . . . . . . . +chr4 53453177 . . . . . . . . . +chr4 57351174 . . . . . . . . . +chr4 58163335 . . . . . . . . . +chr4 62324439 . . . . . . . . . +chr4 63117595 . . . . . . . . . +chr4 63120747 . . . . . . . . . +chr4 65265851 . . . . . . . . . +chr4 65266046 . . . . . . . . . +chr4 70039222 . . . . . . . . . +chr4 80978722 . . . . . . . . . +chr4 83963547 . . . . . . . . . +chr4 84031308 . . . . . . . . . +chr4 95598334 . . . . . . . . . +chr4 97441884 . . . . . . . . . +chr4 98327543 . . . . . . . . . +chr5 102171703 . . . . . . . . . +chr5 102846906 . . . . . . . . . +chr5 103816943 . . . . . . . . . +chr5 103824902 . . . . . . . . . +chr5 104025747 . . . . . . . . . +chr5 111739454 . . . . . . . . . +chr5 114623119 . . . . . . . . . +chr5 115329525 . . . . . . . . . +chr5 115521850 . . . . . . . . . +chr5 115997785 . . . . . . . . . +chr5 124428096 . . . . . . . . . +chr5 124616438 . . . . . . . . . +chr5 12506043 . . . . . . . . . +chr5 125870085 . . . . . . . . . +chr5 135053576 . . . . . . . . . +chr5 136097865 . . . . . . . . . +chr5 136723239 . . . . . . . . . +chr5 141131567 . . . . . . . . . +chr5 143585307 . . . . . . . . . +chr5 147072751 . . . . . . . . . +chr5 147072865 . . . . . . . . . +chr5 147910495 . . . . . . . . . +chr5 15052325 . . . . . . . . . +chr5 15112758 . . . . . . . . . +chr5 21697850 . . . . . . . . . +chr5 23158397 . . . . . . . . . +chr5 23977791 . . . . . . . . . +chr5 32423622 . . . . . . . . . +chr5 35245832 . . . . . . . . . +chr5 35342159 . . . . . . . . . +chr5 50430918 . . . . . . . . . +chr5 51959859 . . . . . . . . . +chr5 58431600 . . . . . . . . . +chr5 64634166 . . . . . . . . . +chr5 65807245 . . . . . . . . . +chr5 66472573 . . . . . . . . . +chr5 72564131 . . . . . . . . . +chr5 73646186 . . . . . . . . . +chr5 87159785 . . . . . . . . . +chr5 90818821 . . . . . . . . . +chr5 99781594 . . . . . . . . . +chr6 100518848 . . . . . . . . . +chr6 103599133 . . . . . . . . . +chr6 113116711 . . . . . . . . . +chr6 121080230 . . . . . . . . . +chr6 127325975 . . . . . . . . . +chr6 127381753 . . . . . . . . . +chr6 127425244 . . . . . . . . . +chr6 128054836 . . . . . . . . . +chr6 128289233 . . . . . . . . . +chr6 128326644 . . . . . . . . . +chr6 128547343 . . . . . . . . . +chr6 134445175 . . . . . . . . . +chr6 134445312 . . . . . . . . . +chr6 143811364 . . . . . . . . . +chr6 146887669 . . . . . . . . . +chr6 147297840 . . . . . . . . . +chr6 17267124 . . . . . . . . . +chr6 33926636 . . . . . . . . . +chr6 37242315 . . . . . . . . . +chr6 47601314 . . . . . . . . . +chr6 49172166 . . . . . . . . . +chr6 51351355 . . . . . . . . . +chr6 56806957 . . . . . . . . . +chr6 67253361 . . . . . . . . . +chr6 76927942 . . . . . . . . . +chr6 83071812 . . . . . . . . . +chr6 83093011 . . . . . . . . . +chr6 86130730 . . . . . . . . . +chr6 87137073 . . . . . . . . . +chr6 87222111 . . . . . . . . . +chr6 94625281 . . . . . . . . . +chr7 104849801 . . . . . . . . . +chr7 117975070 . . . . . . . . . +chr7 119647132 . . . . . . . . . +chr7 119813749 . . . . . . . . . +chr7 120393123 . . . . . . . . . +chr7 120874367 . . . . . . . . . +chr7 123336714 . . . . . . . . . +chr7 125720143 . . . . . . . . . +chr7 126039427 . . . . . . . . . +chr7 127004913 . . . . . . . . . +chr7 128854935 . . . . . . . . . +chr7 128984541 . . . . . . . . . +chr7 134819118 . . . . . . . . . +chr7 135696903 . . . . . . . . . +chr7 137484210 . . . . . . . . . +chr7 137768001 . . . . . . . . . +chr7 138009297 . . . . . . . . . +chr7 138123566 . . . . . . . . . +chr7 138123699 . . . . . . . . . +chr7 139426142 . . . . . . . . . +chr7 146041529 . . . . . . . . . +chr7 147156352 . . . . . . . . . +chr7 148379180 . . . . . . . . . +chr7 148379362 . . . . . . . . . +chr7 148629281 . . . . . . . . . +chr7 150571560 . . . . . . . . . +chr7 152450338 . . . . . . . . . +chr7 152450519 . . . . . . . . . +chr7 16562058 . . . . . . . . . +chr7 16894872 . . . . . . . . . +chr7 17429367 . . . . . . . . . +chr7 20044401 . . . . . . . . . +chr7 26061110 . . . . . . . . . +chr7 26574315 . . . . . . . . . +chr7 28010205 . . . . . . . . . +chr7 30227710 . . . . . . . . . +chr7 30256558 . . . . . . . . . +chr7 35861923 . . . . . . . . . +chr7 56809068 . . . . . . . . . +chr7 87336398 . . . . . . . . . +chr7 88092779 . . . . . . . . . +chr7 89920499 . . . . . . . . . +chr8 10576464 . . . . . . . . . +chr8 107426996 . . . . . . . . . +chr8 109087961 . . . . . . . . . +chr8 109275046 . . . . . . . . . +chr8 109334564 . . . . . . . . . +chr8 113806188 . . . . . . . . . +chr8 119851483 . . . . . . . . . +chr8 121354388 . . . . . . . . . +chr8 129127362 . . . . . . . . . +chr8 129549456 . . . . . . . . . +chr8 13548998 . . . . . . . . . +chr8 13668465 . . . . . . . . . +chr8 14306960 . . . . . . . . . +chr8 17594804 . . . . . . . . . +chr8 19919526 . . . . . . . . . +chr8 19924810 . . . . . . . . . +chr8 22870138 . . . . . . . . . +chr8 23921280 . . . . . . . . . +chr8 24206095 . . . . . . . . . +chr8 34068894 . . . . . . . . . +chr8 37107644 . . . . . . . . . +chr8 4586605 . . . . . . . . . +chr8 70850825 . . . . . . . . . +chr8 71717281 . . . . . . . . . +chr8 73173598 . . . . . . . . . +chr8 73183558 . . . . . . . . . +chr8 73297497 . . . . . . . . . +chr8 81256455 . . . . . . . . . +chr8 86143616 . . . . . . . . . +chr8 87180694 . . . . . . . . . +chr8 88126748 . . . . . . . . . +chr8 93828640 . . . . . . . . . +chr8 97699878 . . . . . . . . . +chr9 100543647 . . . . . . . . . +chr9 103988283 . . . . . . . . . +chr9 106273656 . . . . . . . . . +chr9 107478162 . . . . . . . . . +chr9 108851463 . . . . . . . . . +chr9 110183808 . . . . . . . . . +chr9 111053664 . . . . . . . . . +chr9 116828689 . . . . . . . . . +chr9 118884586 . . . . . . . . . +chr9 120883928 . . . . . . . . . +chr9 123371104 . . . . . . . . . +chr9 13408238 . . . . . . . . . +chr9 14466849 . . . . . . . . . +chr9 14480293 . . . . . . . . . +chr9 24346538 . . . . . . . . . +chr9 3258857 . . . . . . . . . +chr9 42777363 . . . . . . . . . +chr9 43528251 . . . . . . . . . +chr9 43585984 . . . . . . . . . +chr9 44215148 . . . . . . . . . +chr9 44307103 . . . . . . . . . +chr9 54460731 . . . . . . . . . +chr9 66728918 . . . . . . . . . +chr9 66794084 . . . . . . . . . +chr9 67556540 . . . . . . . . . +chr9 70477636 . . . . . . . . . +chr9 72497695 . . . . . . . . . +chr9 72916030 . . . . . . . . . +chr9 74815214 . . . . . . . . . +chr9 75371664 . . . . . . . . . +chr9 8033087 . . . . . . . . . +chr9 8055015 . . . . . . . . . +chr9 83462792 . . . . . . . . . +chr9 86714892 . . . . . . . . . +chrX 109484691 . . . . . . . . . +chrX 137172820 . . . . . . . . . +chrX 139917606 . . . . . . . . . +chrX 140401017 . . . . . . . . . +chrX 163589625 . . . . . . . . . +chrX 166360754 . . . . . . . . . +chrX 166427362 . . . . . . . . . +chrX 166432950 . . . . . . . . . +chrX 84483714 . . . . . . . . . +chrX 98516735 . . . . . . . . . diff -r 000000000000 -r d9c1f2133124 tool-data/rnachipintegrator_canonical_genes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rnachipintegrator_canonical_genes.loc.sample Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,19 @@ +#This is a sample file distributed with Galaxy that is used by the +#rnachipintegrator_canonical_genes tool. The file has this format (white space +#characters are TAB characters): +# +# +# +#For example: +# +#hg18_Gm12878_Ctcf hg18 Gm12878/Ctcf /genomes/hg18/Gm12878_Ctcf.tsv +#hg19_Gm12878_H3k27ac hg19 Gm12878/H3k27ac /genomes/hg19/Gm12878_H3k27ac.tsv +#mm9_Gm12878_H3k27me3 mm9 Gm12878/H3k27me3 /genomes/mm9/Gm12878_H3k27me3.tsv +#...etc... +# +#The gene list files should contain the gene symbol, chromosome, start and end +#positions, and strand for each gene in the list. +# +#This file should be placed in galaxy's tool-data directory when the +#rnachipintegrator_canonical_genes tool is installed. + diff -r 000000000000 -r d9c1f2133124 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,6 @@ + + + value, dbkey, name, path + +
+ diff -r 000000000000 -r d9c1f2133124 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,74 @@ + + + + + + https://pypi.python.org/packages/source/x/xlwt/xlwt-0.7.5.tar.gz + $INSTALL_DIR/lib/python + + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + + + $INSTALL_DIR/lib/python + $INSTALL_DIR/bin + + + + Installs Python module xlwt 0.7.5 + + + + + https://pypi.python.org/packages/source/x/xlrd/xlrd-0.9.3.tar.gz + $INSTALL_DIR/lib/python + + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + + + $INSTALL_DIR/lib/python + $INSTALL_DIR/bin + + + + Installs Python module xlrd 0.9.3 + + + + + https://pypi.python.org/packages/source/x/xlutils/xlutils-1.7.1.tar.gz + $INSTALL_DIR/lib/python + + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + + + $INSTALL_DIR/lib/python + $INSTALL_DIR/bin + + + + Installs Python module xlutils 1.7.1 + + + + + https://github.com/fls-bioinformatics-core/RnaChipIntegrator/archive/v0.4.4.tar.gz + + RnaChipIntegrator.py + $INSTALL_DIR + + + Spreadsheet.py + $INSTALL_DIR + + + $INSTALL_DIR + $INSTALL_DIR + + + + Installs RnaChipIntegrator 0.4.3 + +