Mercurial > repos > pjbriggs > rnachipintegrator
changeset 0:d9c1f2133124 draft
Uploaded initial version 0.4.4.
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--- /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: + + <tool file="rnachipintegrator/rnachipintegrator_wrapper.xml" /> + <tool file="rnachipintegrator/rnachipintegrator_canonical_genes.xml" /> + +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: + + <datatype extension="xls" type="galaxy.datatypes.data:Data" mimetype="application/vnd.ms-excel" /> + +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.
--- /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)) +
--- /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 @@ +<tool id="data_manager_rnachipintegrator_fetch_canonical_genes" name="Fetch RnaChipIntegrator canonical genes" version="0.0.1" tool_type="manage_data"> + <description>Fetch and install canonical gene lists for RnaChipIntegrator</description> + <command interpreter="python">data_manager_rnachipintegrator_fetch_canonical_genes.py + "${out_file}" + "${description}"</command> + <inputs> + <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> + <param type="text" name="unique_id" label="Internal identifier" + help="Identifier string to associate with the annotation e.g. 'mm9_generic'" /> + <param type="text" name="description" value="" + label="Description of canonical gene list" size="50" + help="Text that will appear in the list of canonical genes" /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="history">History</option> + <option value="server">File on the server</option> + </param> + <when value="server"> + <param type="text" name="gene_list_filename" value="" size="50" + label="Full path to the canonical genes file on disk" optional="False" /> + <param type="boolean" name="create_symlink" + truevalue="create_symlink" falsevalue="copy_file" + label="Create symlink to orignal data instead of copying" checked="False" /> + </when> + <when value="history"> + <param name="input_gene_list" type="data" format="tabular" + label="Canonical gene list from history" optional="False" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <test> + <param name="dbkey" value="mm9"/> + <param name="description" value="Mouse (mm9)"/> + <param name="reference_source_selector" value="history"/> + <param name="input_gene_list" value="mm9_canonical_genes.tsv"/> + <output name="out_file" file="mm9_canonical_genes.data_manager_json"/> + </test> + </tests> + <help> + +.. 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.) + </help> +</tool>
--- /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 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml" id="data_manager_rnachipintegrator_fetch_canonical_genes"> + <data_table name="rnachipintegrator_canonical_genes"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file" > + <move type="file"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rnachipintegrator/${dbkey}/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rnachipintegrator/${dbkey}/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers>
--- /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 @@ +<tool id="rnachipintegrator_canonical_genes" name="Analyse canonical genes against ChIP data" version="@VERSION@-0"> + <description>using RnaChipIntegrator</description> + <macros> + <import>rnachipintegrator_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command interpreter="bash">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 + </command> + <inputs> + <param format="tabular" name="chipseq" type="data" label="ChIP peaks data file" /> + <param name="canonical_genes" type="select" label="Canonical genes to analyse ChIP peaks against"> + <options from_data_table="rnachipintegrator_canonical_genes"> + </options> + </param> + <conditional name="analysis_options"> + <!-- user must specify if ChIP peaks are summits or regions --> + <param name="peak_type" type="select" label="ChIP peaks are" + help="Options and outputs depend on whether ChIP data are summits or regions"> + <option value="summits">summits</option> + <option value="regions">regions</option> + </param> + <when value="summits"> + <param name="window" type="integer" value="20000" optional="true" + label="Maximum distance a peak can be from each transcript + TSS before being omitted from analysis" /> + <param name="cutoff" type="integer" value="130000" optional="true" + label="Maximum distance a transcript TSS can be from each + peak before being omitted from the analysis" /> + </when> + <when value="regions"> + <param name="edge_cutoff" type="integer" value="10000" optional="true" + label="Maximum distance a transcript edge can be from the + peak edge before being omitted from the analysis" + help="Set to zero to indicate that no cut off should be applied" /> + <param name="number" type="integer" value="4" optional="true" + label="Maximum number of transcripts per peak to report from + from the analysis" /> + <param name="promoter_start" type="integer" value="-10000" optional="true" + label="Start of promoter region with respect to gene TSS" /> + <param name="promoter_end" type="integer" value="2500" optional="true" + label="End of promoter region with respect to gene TSS" /> + <param name="pad_output" type="boolean" checked="false" truevalue="yes" + label="Output same number of lines for each peak (--pad)" + help="Add blank lines in output for peaks with fewer than maximum number + of hits" /> + </when> + </conditional> + <param name="results_as_zip" type="boolean" checked="false" truevalue="yes" + label="Put output tab-delimited files into a single zip archive" /> + </inputs> + <outputs> + <!-- Always produce XLS output --> + <data format="xls" name="xls_output" + label="All RnaChipIntegrator analyses for ${canonical_genes.fields.name} vs ${chipseq.name} (Excel spreadsheet)" /> + <!-- Outputs only produced for summit data --> + <data format="tabular" name="peaks_to_transcripts_out" + label="Nearest summits to transcripts for ${canonical_genes.fields.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "summits"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="tabular" name="tss_to_summits_out" + label="Nearest summits to TSS for ${canonical_genes.fields.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "summits"</filter> + <filter>results_as_zip is False</filter> + </data> + <!-- Outputs only produced for peak data --> + <data format="tabular" name="transcripts_to_edges_out" + label="Nearest transcripts to peak edges for ${canonical_genes.fields.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "regions"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="tabular" name="transcripts_to_edges_summary" + label="Nearest transcripts to peak edges (summary) for ${canonical_genes.fields.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "regions"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="tabular" name="tss_to_edges_out" + label="Nearest TSS to peak edges for ${canonical_genes.fields.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "regions"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="tabular" name="tss_to_edges_summary" + label="Nearest TSS to peak edges (summary) for ${canonical_genes.fields.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "regions"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="zip" name="zip_file" + label="All tab-delimited files for ${canonical_genes.fields.name} vs ${chipseq.name} (zip file)" > + <filter>results_as_zip is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="chipseq" value="mm9_summits.txt" /> + <param name="canonical_genes" value="mm9_test" /> + <param name="peak_type" value="summits" /> + <param name="window" value="50000" /> + <param name="cutoff" value="130000" /> + <output name="xls_output" file="mm9_summits.xls" compare="sim_size" /> + <output name="peaks_to_transcripts_out" file="mm9_summits_to_transcripts.out" ftype="tabular" /> + <output name="tss_to_summits_out" file="mm9_tss_to_summits.out" ftype="tabular" /> + </test> + <test> + <param name="chipseq" value="mm9_peaks.txt" /> + <param name="canonical_genes" value="mm9_test" /> + <param name="peak_type" value="regions" /> + <param name="edge_cutoff" value="50000" /> + <output name="xls_output" file="mm9_peaks.xls" compare="sim_size" /> + <output name="transcripts_to_edges_out" file="mm9_transcripts_to_edges.out" ftype="tabular" /> + <output name="transcripts_to_edges_summary" file="mm9_transcripts_to_edges.summary" ftype="tabular" /> + <output name="tss_to_edges_out" file="mm9_tss_to_edges.out" ftype="tabular" /> + <output name="tss_to_edges_summary" file="mm9_tss_to_edges.summary" ftype="tabular" /> + </test> + </tests> + <help> + +.. 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. + </help> +</tool>
--- /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 @@ +<macros> + <token name="@VERSION@">0.4.4</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.7.5">python_xlwt</requirement> + <requirement type="package" version="0.9.3">python_xlrd</requirement> + <requirement type="package" version="1.7.1">python_xlutils</requirement> + <requirement type="package" version="0.4.4">rnachipintegrator</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>rnachipintegrator --version</version_command> + </xml> +</macros>
--- /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] <rnaseq_in> <chipseq_in> --output_xls <xls_out> +# +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
--- /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 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="rnachipintegrator_wrapper" name="RnaChipIntegrator" version="@VERSION@-0"> + <description>Integrated analysis of gene expression data and ChIP data</description> + <macros> + <import>rnachipintegrator_macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command interpreter="bash">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 + </command> + <inputs> + <param format="tabular" name="rnaseq" type="data" label="Gene expression data file" /> + <param format="tabular" name="chipseq" type="data" label="ChIP peaks data file" /> + <conditional name="analysis_options"> + <!-- user must specify if ChIP peaks are summits or regions --> + <param name="peak_type" type="select" label="ChIP peaks are" + help="Options and outputs depend on whether ChIP data are summits or regions"> + <option value="summits">summits</option> + <option value="regions">regions</option> + </param> + <when value="summits"> + <param name="window" type="integer" value="20000" optional="true" + label="Maximum distance a peak can be from each transcript + TSS before being omitted from analysis" /> + <param name="cutoff" type="integer" value="130000" optional="true" + label="Maximum distance a transcript TSS can be from each + peak before being omitted from the analysis" /> + </when> + <when value="regions"> + <param name="edge_cutoff" type="integer" value="10000" optional="true" + label="Maximum distance a transcript edge can be from the + peak edge before being omitted from the analysis" + help="Set to zero to indicate that no cut off should be applied" /> + <param name="number" type="integer" value="4" optional="true" + label="Maximum number of transcripts per peak to report from + from the analysis" /> + <param name="promoter_start" type="integer" value="-10000" optional="true" + label="Start of promoter region with respect to gene TSS" /> + <param name="promoter_end" type="integer" value="2500" optional="true" + label="End of promoter region with respect to gene TSS" /> + <param name="pad_output" type="boolean" checked="false" truevalue="yes" + label="Output same number of lines for each peak" + help="Add blank lines in output for peaks with fewer than maximum number + of hits (--pad)" /> + </when> + </conditional> + <param name="results_as_zip" type="boolean" checked="false" truevalue="yes" + label="Put output tab-delimited files into a single zip archive" /> + </inputs> + <outputs> + <!-- Always produce XLS output --> + <data format="xls" name="xls_output" + label="All RnaChipIntegrator analyses for ${rnaseq.name} vs ${chipseq.name} (Excel spreadsheet)" /> + <!-- Outputs only produced for summit data --> + <data format="tabular" name="peaks_to_transcripts_out" + label="Nearest summits to transcripts for ${rnaseq.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "summits"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="tabular" name="tss_to_summits_out" + label="Nearest TSS to summits for ${rnaseq.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "summits"</filter> + <filter>results_as_zip is False</filter> + </data> + <!-- Outputs only produced for peak data --> + <data format="tabular" name="transcripts_to_edges_out" + label="Nearest transcripts to peak edges for ${rnaseq.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "regions"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="tabular" name="transcripts_to_edges_summary" + label="Nearest transcripts to peak edges (summary) for ${rnaseq.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "regions"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="tabular" name="tss_to_edges_out" + label="Nearest TSS to peak edges for ${rnaseq.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "regions"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="tabular" name="tss_to_edges_summary" + label="Nearest TSS to peak edges (summary) for ${rnaseq.name} vs ${chipseq.name}" > + <filter>analysis_options['peak_type'] == "regions"</filter> + <filter>results_as_zip is False</filter> + </data> + <data format="zip" name="zip_file" + label="All tab-delimited files for ${rnaseq.name} vs ${chipseq.name} (zip file)" > + <filter>results_as_zip is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="rnaseq" value="ExpressionData.txt" ftype="tabular" /> + <param name="chipseq" value="ChIP_summits.txt" ftype="tabular" /> + <param name="peak_type" value="summits" /> + <param name="window" value="20000" /> + <param name="cutoff" value="130000" /> + <!-- + **NB** outputs have to be specified in order that they appear in the + tool (which is the order they will be written to the history) - the + test framework seems to use the order and ignores the "name" attribute + --> + <output name="xls_output" file="summits.xls" compare="sim_size" /> + <output name="peaks_to_transcripts_out" file="peaks_to_transcripts.out" ftype="tabular" /> + <output name="tss_to_summits_out" file="tss_to_summits.out" ftype="tabular" /> + </test> + <test> + <param name="rnaseq" value="ExpressionData.txt" ftype="tabular" /> + <param name="chipseq" value="ChIP_peaks.txt" ftype="tabular" /> + <param name="peak_type" value="regions" /> + <param name="edge_cutoff" value="130000" /> + <!-- + **NB** outputs have to be specified in order that they appear in the + tool (which is the order they will be written to the history) - the + test framework seems to use the order and ignores the "name" attribute + --> + <output name="xls_output" file="peaks.xls" compare="sim_size" /> + <output name="transcripts_to_edges_out" file="transcripts_to_edges.out" ftype="tabular" /> + <output name="transcripts_to_edges_summary" file="transcripts_to_edges.summary" ftype="tabular" /> + <output name="tss_to_edges_out" file="tss_to_edges.out" ftype="tabular" /> + <output name="tss_to_edges_summary" file="tss_to_edges.summary" ftype="tabular" /> + </test> + </tests> + <help> + +.. 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. + </help> +</tool>
--- /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 167222964 167223261 +chr1 167906284 167906554 +chr1 170255081 170255260 +chr1 17030405 17030545 +chr1 172620779 172620912 +chr1 172620917 172621080 +chr1 174376470 174376659 +chr1 181061299 181061446 +chr1 182479646 182479905 +chr1 185854947 185855105 +chr1 194258648 194259032 +chr1 194645118 194645475 +chr1 194957396 194957723 +chr1 195324443 195324741 +chr1 195330701 195330930 +chr1 195338316 195338616 +chr1 195342728 195342985 +chr1 195384767 195385195 +chr1 197057796 197057843 +chr1 24609562 24609623 +chr1 24609923 24609992 +chr1 24730996 24731077 +chr1 26734195 26734485 +chr1 34206924 34207100 +chr1 36106813 36107058 +chr1 39492140 39492513 +chr1 40325917 40326123 +chr1 44195449 44195639 +chr1 52625416 52625560 +chr1 54631692 54631815 +chr1 55283572 55283675 +chr1 63664888 63665018 +chr1 72769824 72770056 +chr1 72770058 72770226 +chr1 72815517 72815742 +chr1 75481920 75482054 +chr1 77457642 77457791 +chr1 78630893 78631160 +chr1 88408969 88409267 +chr1 89989553 89989714 +chr1 90412932 90413132 +chr1 90592499 90592629 +chr1 91496003 91496145 +chr1 91496155 91496319 +chr1 92070253 92070431 +chr1 95186508 95186637 +chr1 9619046 9619167 +chr1 9619175 9619382
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ChIP_summits.txt Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,654 @@ +#peak mid plus1 +chr10 106033584 106033585 +chr10 106033751 106033752 +chr10 107429926 107429927 +chr10 114752719 114752720 +chr10 114994096 114994097 +chr10 127058840 127058841 +chr10 127184557 127184558 +chr10 13089536 13089537 +chr10 13408622 13408623 +chr10 17725474 17725475 +chr10 21862583 21862584 +chr10 21862774 21862775 +chr10 31587625 31587626 +chr10 41613298 41613299 +chr10 43640892 43640893 +chr10 43740181 43740182 +chr10 45093322 45093323 +chr10 57702300 57702301 +chr10 59362596 59362597 +chr10 59693654 59693655 +chr10 60613588 60613589 +chr10 60696228 60696229 +chr10 67567003 67567004 +chr10 76664902 76664903 +chr10 7707698 7707699 +chr10 79808095 79808096 +chr10 80126390 80126391 +chr10 81033719 81033720 +chr10 82306942 82306943 +chr10 82517145 82517146 +chr10 84922053 84922054 +chr10 88433836 88433837 +chr10 89195191 89195192 +chr10 93642365 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ExpressionData.txt Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +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 - 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0 +NM_207228_Tsga10 chr1 37783457 37922148 - 0 +NM_207233_C1ql2 chr1 122196386 122239751 + 0 +NM_207281_4832428D23Rik chr1 44260915 44515719 - 0 +NM_207583_Fam5b chr1 160175402 160286644 - 0 +NM_207653_Cflar chr1 58768296 58813658 + 0 +NM_207653_Cflar chr1 58813703 58815725 + 0 +NM_213616_Atp2b4 chr1 135602265 135697538 - 0 +NR_002840_Gas5 chr1 162964758 162968663 + 0 +NR_002858_EG241041 chr1 21268965 21306401 - 0 +NR_002870_Dnm3os chr1 164119785 164155671 + 0 +NR_003623_EG277333 chr1 182251970 182262902 - 0 +NR_026896_4931440L10Rik chr1 136437533 136449760 - 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_canonical_genes.data_manager_json Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,1 @@ +{"data_tables": {"rnachipintegrator_canonical_genes": {"value": "dataset_62.dat", "name": "Mouse (mm9)", "dbkey": "mm9"}}}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_canonical_genes.tsv Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,10 @@ +mm9.kgXref.geneSymbol #mm9.knownCanonical.chrom mm9.knownCanonical.chromStart mm9.knownCanonical.chromEnd mm9.knownGene.strand mm9.knownCanonical.transcript mm9.kgXref.refseq +Xkr4 chr1 3204562 3661579 - uc007aeu.1 NM_001011874 +AK149000 chr1 3638391 3648985 - uc007aev.1 +Rp1 chr1 4333587 4350395 - uc007aex.2 NM_011283 +Sox17 chr1 4481008 4486494 - uc007aez.1 NM_011441 +Mrpl15 chr1 4763278 4775807 - uc007aff.2 NM_001177658 +Lypla1 chr1 4797973 4836816 + uc007afh.1 NM_008866 +Tcea1 chr1 4847774 4887990 + uc007afi.2 NM_011541 +Rgs20 chr1 4899656 5060366 - uc007afl.2 NM_001177795 +Atp6v1h chr1 5073253 5152630 + uc007afn.1 NM_133826
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_peaks.txt Tue Jun 30 06:44:06 2015 -0400 @@ -0,0 +1,500 @@ +chr1 3213477 3213513 +chr1 3542857 3542893 +chr1 3560979 3561015 +chr1 3621547 3621583 +chr1 4630453 4630489 +chr1 5261737 5261773 +chr1 5562257 5562293 +chr1 6926999 6927035 +chr1 7262846 7262882 +chr1 7322487 7322523 +chr1 7666187 7666223 +chr1 7744070 7744106 +chr1 7969291 7969327 +chr1 8421057 8421093 +chr1 8679021 8679057 +chr1 9359611 9359647 +chr1 9415439 9415475 +chr1 9608130 9608166 +chr1 9616803 9616839 +chr1 9897397 9897433 +chr1 10251725 10251761 +chr1 10254195 10254231 +chr1 10305254 10305290 +chr1 10451286 10451322 +chr1 11340573 11340609 +chr1 11610483 11610519 +chr1 11960381 11960417 +chr1 11987310 11987346 +chr1 12441678 12441714 +chr1 12704380 12704416 +chr1 12871650 12871686 +chr1 13179280 13179316 +chr1 13934524 13934560 +chr1 14479277 14479313 +chr1 14755996 14756032 +chr1 14848637 14848673 +chr1 14967919 14967955 +chr1 15097029 15097065 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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 +chr1 138237818 138237819 +chr1 138288739 138288740 +chr1 138701415 138701416 +chr1 138883160 138883161 +chr1 139093105 139093106 +chr1 139286502 139286503 +chr1 139448680 139448681 +chr1 139944056 139944057 +chr1 140207040 140207041 +chr1 141517452 141517453 +chr1 142087663 142087664 +chr1 142561476 142561477 +chr1 142732555 142732556 +chr1 142765329 142765330 +chr1 142811575 142811576 +chr1 142823331 142823332 +chr1 142985887 142985888 +chr1 143071919 143071920 +chr1 143137676 143137677 +chr1 143684082 143684083 +chr1 143803869 143803870 +chr1 143866547 143866548 +chr1 144585588 144585589 +chr1 145018626 145018627 +chr1 145169340 145169341 +chr1 145286043 145286044 +chr1 145743816 145743817 +chr1 145793073 145793074 +chr1 145943835 145943836 +chr1 145973347 145973348 +chr1 146233793 146233794 +chr1 146349912 146349913 +chr1 146992848 146992849 +chr1 147015972 147015973 +chr1 147919367 147919368 +chr1 148073000 148073001 +chr1 148184896 148184897 +chr1 148571263 148571264 +chr1 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
--- /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 --- --- ---
--- /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
--- /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
--- /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
--- /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
--- /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 . . . . . . . . . +chr1 72692566 . . . . . . . . . +chr1 73777980 . . . . . . . . . +chr1 73785621 . . . . . . . . . +chr1 73888393 . . . . . . . . . +chr1 74405639 . . . . . . . . . +chr1 74847215 . . . . . . . . . +chr1 75153395 . . . . . . . . . +chr1 75851063 . . . . . . . . . +chr1 76061520 . . . . . . . . . +chr1 76206645 . . . . . . . . . +chr1 76479779 . . . . . . . . . +chr1 76831245 . . . . . . . . . +chr1 76909640 . . . . . . . . . +chr1 76974470 . . . . . . . . . +chr1 76982172 . . . . . . . . . +chr1 77062655 . . . . . . . . . +chr1 77544118 . . . . . . . . . +chr1 77659070 . . . . . . . . . +chr1 78599048 . . . . . . . . . +chr1 78675935 . . . . . . . . . +chr1 78996093 . . . . . . . . . +chr1 79237126 . . . . . . . . . +chr1 79266617 . . . . . . . . . +chr1 79628362 . . . . . . . . . +chr1 80005541 . . . . . . . . . +chr1 80025898 . . . . . . . . . +chr1 80028050 . . . . . . . . . +chr1 80852217 . . . . . . . . . +chr1 80913955 . . . . . . . . . +chr1 81161437 . . . . . . . . . +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 . . . . . . . . .
--- /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 +BC043098_Fam168b chr1 34870072 34917183 - 1 0 +BC049091_D1Bwg0212e chr1 39592545 39603734 + 1 0 +BC049713_Ankrd45 chr1 163072817 163099826 + 1 0 +BC050813_4921511C04Rik chr1 37157481 37244861 + 1 0 +BC051128_4921521F21Rik chr1 65059273 65079312 - 1 0 +BC052693_2810422O20Rik chr1 165924541 165927371 + 1 0 +BC052931_A630001G21Rik chr1 87601462 87674840 - 1 0 +BC053100_5730559C18Rik chr1 138110108 138130841 - 1 0 +BC054802_9630058J23Rik chr1 181476521 181558044 + 1 0 +BC055845_2810025M15Rik chr1 159342483 159350353 + 1 0 +BC055955_A130010J15Rik chr1 194999663 195004015 + 1 0 +BC057872_Rab3gap2 chr1 187028006 187110623 + 1 0 +BC058417_2610017I09Rik chr1 42648822 42751667 - 1 0 +BC059254_Phlpp chr1 108042052 108306367 + 1 0 +BC070435_Fam123c chr1 34620070 34671545 + 1 0 +BC070446_Fam135a chr1 24017617 24107170 - 1 0 +BC071241_9430016H08Rik chr1 57463192 57497936 + 1 0 +BC072639_2010300C02Rik chr1 37646877 37776659 - 1 0 +BC080290_5033414K04Rik chr1 84032539 84360735 - 0 0 +BC082310_9430031J16Rik chr1 81073525 81338329 + 0 0 +BC089525_2310007B03Rik chr1 95047933 95063386 - 0 0 +BC089561_Cep350 chr1 157692096 157820375 - 0 0 +BC147491_A230074B11Rik chr1 37083441 37133840 + 0 0 +BC147657_9630028B13Rik chr1 187253234 187265698 - 0 0 +ENSMUST00000027997_Rgs5 chr1 171625108 171625913 + 0 0 +ENSMUST00000051203_1700001G17Rik chr1 33726669 33727551 + 0 0 +ENSMUST00000054333_A130050O07Rik chr1 139823828 139826840 + 0 0 +ENSMUST00000056879_C230029F24Rik chr1 49301475 49397265 + 0 0 +ENSMUST00000057543_A730013G03Rik chr1 194659323 194661397 - 0 0 +ENSMUST00000062637_4930470H14Rik chr1 175156866 175201240 + 0 0 +ENSMUST00000070048_ENSMUSG00000056128 chr1 92571736 92576368 + 0 0 +ENSMUST00000070987_EG433384 chr1 183781705 183783320 - 0 0 +ENSMUST00000072395_Olfr1406 chr1 175113651 175120746 - 0 0 +ENSMUST00000094288_Wdr64 chr1 177654798 177798070 + 0 0 +ENSMUST00000094950_Pgap1 chr1 54529849 54614539 - 0 0 +ENSMUST00000097776_Cnnm3 chr1 36567938 36585164 + 0 0 +EU429481_Igfn1 chr1 137825893 137890307 - 0 0 +FJ024495_Ildr2 chr1 168236882 168239692 - 0 0 +FJ210934_Unc80 chr1 66514856 66556109 + 0 0 +NM_001001565_Chpf chr1 75470923 75476437 - 0 0 +NM_001001809_Olfr218 chr1 175130421 175134469 + 0 0 +NM_001001883_Hecw2 chr1 53867026 54252002 - 0 0 +NM_001003917_Atg9a chr1 75177439 75189181 - 0 0 +NM_001004173_Sgpp2 chr1 78306692 78416864 + 0 0 +NM_001005423_Mreg chr1 72170192 72258895 - 0 0 +NM_001005507_Smg7 chr1 154684125 154750410 - 0 0 +NM_001005508_Arhgap30 chr1 173319072 173340822 + 0 0 +NM_001005520_Olfr244 chr1 176032571 176067605 - 0 0 +NM_001008419_Aox3l1 chr1 58335180 58437083 + 0 0 +NM_001008426_EG433365 chr1 155721475 155724001 + 0 0 +NM_001008533_Adora1 chr1 136095799 136181661 - 0 0 +NM_001009940_Il19 chr1 132786042 132915234 - 0 0 +NM_001011525_Olfr1415 chr1 94376258 94381054 - 0 0 +NM_001011525_Olfr1415 chr1 94407669 94418761 - 0 0 +NM_001011684_Nms chr1 38995917 39007113 + 0 0 +NM_001011873_Xkr9 chr1 13658862 13691794 + 0 0 +NM_001011874_Xkr4 chr1 3203722 3713108 - 0 0 +NM_001012330_Zfp238 chr1 179359958 179380892 + 0 0 +NM_001013374_Lman2l chr1 36362897 36502078 - 0 0 +NM_001013382_Lrrc52 chr1 169375806 169397136 - 0 0 +NM_001013771_Gm973 chr1 59573136 59693241 + 0 0 +NM_001013779_Aim2 chr1 175385835 175396165 + 0 0 +NM_001014974_Ttll4 chr1 74708314 74748400 + 0 0 +NM_001024721_BC094916 chr1 175451304 175466101 - 0 0 +NM_001024945_Qsox1 chr1 157625296 157670499 - 0 0 +NM_001025156_Ccdc93 chr1 123208865 123403037 + 0 0 +NM_001025565_Lhx9 chr1 140694768 140740509 - 0 0 +NM_001025602_Il1rl1 chr1 40462708 40522260 + 0 0 +NM_001029984_Fcrlb chr1 172836813 172843072 - 0 0 +NM_001037170_Tomm40l chr1 173147934 173152645 - 0 0 +NM_001037725_Fam117b chr1 59937517 60042190 + 0 0 +NM_001037918_Lipt1 chr1 37928603 37934232 + 0 0 +NM_001037999_Dbi chr1 122009883 122046068 - 0 0 +NM_001038592_Glrx2 chr1 145585774 145608282 + 0 0 +NM_001038619_Dnm3 chr1 163902671 164408155 - 0 0 +NM_001039126_Asb1 chr1 93437143 93461729 + 0 0 +NM_001039472_Kif21b chr1 138027986 138074578 + 0 0 +NM_001039475_Slco6b1 chr1 98802763 98894139 - 0 0 +NM_001039482_Klhl20 chr1 163018528 163061699 - 0 0 +NM_001039483_Tmco1 chr1 169238419 169279112 + 0 0 +NM_001039484_Kcnj10 chr1 174258852 174304216 + 0 0 +NM_001039493_Plekhm3 chr1 64832557 65032270 - 0 0 +NM_001039495_Ccdc108 chr1 74947239 74982168 - 0 0 +NM_001039509_Pnkd chr1 74331504 74400245 + 0 0 +NM_001039710_Coq10b chr1 55101051 55129538 + 0 0 +NM_001039934_Mtap2 chr1 66187374 66489157 + 0 0 +NM_001042634_Clk1 chr1 58467034 58480936 - 0 0 +NM_001045481_Ifi203 chr1 175804708 175928457 - 0 0 +NM_001077189_Fcgr2b chr1 172890316 172916060 - 0 0 +NM_001077353_Gsta3 chr1 21230690 21255722 + 0 0 +NM_001077403_Nrp2 chr1 62724499 63100251 + 0 0 +NM_001081023_Cacna1s chr1 137949297 138016348 + 0 0 +NM_001081078_Lct chr1 130174327 130224881 - 0 0 +NM_001081079_Ogfrl1 chr1 23278472 23451348 - 0 0 +NM_001081259_Mfsd7b chr1 192825304 192850534 - 0 0 +NM_001081275_1700009P17Rik chr1 173032694 173057075 + 0 0 +NM_001081361_Mosc1 chr1 186610666 186635172 - 0 0 +NM_001081756_E030049G20Rik chr1 128277776 128727190 - 0 0 +NM_001082573_Crygc chr1 65118108 65146863 - 0 0 +NM_001083897_Mpzl1 chr1 167522314 167564669 - 0 0 +NM_001085409_Steap3 chr1 122037552 122169282 - 0 0 +NM_001099637_Cep170 chr1 178663793 178744307 - 0 0 +NM_001103182_Lin9 chr1 182572002 182620816 + 0 0 +NM_001105667_Dtymk chr1 95689006 95698492 - 0 0 +NM_001110783_Ank1 chr1 77759424 77766452 - 0 0 +NM_001110831_Dnpep chr1 75304471 75314673 - 0 0 +NM_001111059_Cd34 chr1 196683888 196826273 + 0 0 +NM_001111279_Wdfy1 chr1 79689958 79772698 - 0 0 +NM_001111314_Ngef chr1 89373415 89470499 - 0 0 +NM_001111316_Ptprc chr1 139959456 140088994 - 0 0 +NM_001111320_Idh1 chr1 65185668 65233033 - 0 0 +NM_001113394_Cd247 chr1 167711216 167807397 + 0 0 +NM_001122685_Rhbdd1 chr1 82313047 82441937 + 0 0 +NM_001126046_Fam178b chr1 36619544 36740008 - 0 0 +NM_001128605_Psen2 chr1 182157140 182247499 - 0 0 +NM_001128609_Dedd chr1 173258959 173273620 + 0 0 +NM_001130174_Tnnt2 chr1 137732931 137748838 + 0 0 +NM_001134829_Lpgat1 chr1 193521144 193605705 + 0 0 +NM_001136070_Lgtn chr1 133049773 133084235 + 0 0 +NM_001142647_Tmem194b chr1 52687569 52708760 + 0 0 +NM_001159649_Lax1 chr1 135575626 135586665 - 0 0 +NM_001159719_Sept2 chr1 95375046 95406820 + 0 0 +NM_001159730_Pdc chr1 152154402 152181077 + 0 0 +NM_007381_Acadl chr1 66861363 66909886 - 0 0 +NM_007415_Parp1 chr1 182499033 182531385 + 0 0 +NM_007422_Adss chr1 179693113 179888685 - 0 0 +NM_007432_Akp3 chr1 89021583 89042994 + 0 0 +NM_007433_Akp5 chr1 88983274 88986861 - 0 0 +NM_007453_Prdx6 chr1 163170243 163210238 - 0 0 +NM_007463_Speg chr1 75371872 75428879 + 0 0 +NM_007495_Astn1 chr1 160292424 160626748 + 0 0 +NM_007498_Atf3 chr1 192994178 193057173 - 0 0 +NM_007525_Bard1 chr1 71076934 71149526 - 0 0 +NM_007561_Bmpr2 chr1 59820296 59927706 + 0 0 +NM_007570_Btg2 chr1 135971251 135991759 - 0 0 +NM_007576_C4bp chr1 132531357 132558199 - 0 0 +NM_007642_Cd28 chr1 60763315 60830749 + 0 0 +NM_007649_Cd48 chr1 173603288 173635385 + 0 0 +NM_007685_Cfc1 chr1 34592493 34601156 + 0 0 +NM_007695_Chi3l1 chr1 136069840 136086738 + 0 0 +NM_007722_Cxcr7 chr1 92100063 92112863 + 0 0 +NM_007733_Col19a1 chr1 24258667 24602262 - 0 0 +NM_007734_Col4a3 chr1 82583506 82718629 + 0 0 +NM_007735_Col4a4 chr1 82438140 82584744 - 0 0 +NM_007737_Col5a2 chr1 45431177 45560226 - 0 0 +NM_007740_Col9a1 chr1 24164692 24268636 + 0 0 +NM_007758_Cr2 chr1 196963005 197003002 - 0 0 +NM_007768_Crp chr1 174620782 174763152 + 0 0 +NM_007774_Cryga chr1 65146986 65150012 - 0 0 +NM_007776_Crygd chr1 65108417 65110024 - 0 0 +NM_007777_Cryge chr1 65095133 65097767 - 0 0 +NM_007791_Csrp1 chr1 137526251 137648807 + 0 0 +NM_007799_Ctse chr1 133534879 133572077 + 0 0 +NM_007827_Daf2 chr1 132285116 132319576 - 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0 0 +NM_145508_Dyrk3 chr1 133018921 133034897 - 0 0 +NM_145509_5430435G22Rik chr1 133585272 133610099 + 0 0 +NM_145510_Rabif chr1 136391105 136405512 + 0 0 +NM_145511_BC003331 chr1 152183263 152240229 - 0 0 +NM_145512_Sft2d2 chr1 167104119 167124549 - 0 0 +NM_145513_Tiprl chr1 167133855 167183116 - 0 0 +NM_145514_Wdr26 chr1 183100306 183150525 - 0 0 +NM_145515_Mark1 chr1 186720345 186823408 - 0 0 +NM_145516_Plekhb2 chr1 34906787 34936422 + 0 0 +NM_145517_Ormdl1 chr1 53353438 53367153 + 0 0 +NM_145518_Ndufs1 chr1 63190187 63223454 - 0 0 +NM_145519_Farp2 chr1 95408676 95518914 + 0 0 +NM_145624_Zfp709 chr1 87911157 87911749 - 0 0 +NM_145692_Lrrc67 chr1 9943781 9999420 - 0 0 +NM_145856_Il17f chr1 20767237 20776566 - 0 0 +NM_145977_Slc45a3 chr1 133859512 133879541 + 0 0 +NM_145991_Cdc73 chr1 145274292 145549936 - 0 0 +NM_145996_Arid5a chr1 36359349 36380874 + 0 0 +NM_146103_Tmem185b chr1 121396063 121425550 + 0 0 +NM_146106_Lyplal1 chr1 187911630 187941208 - 0 0 +NM_146107_Actr1b chr1 36754975 36766847 - 0 0 +NM_146108_Hibch chr1 52899113 52977830 + 0 0 +NM_146110_Aamp chr1 74326421 74331613 - 0 0 +NM_146112_Gigyf2 chr1 89223593 89347370 + 0 0 +NM_146250_Gpr1 chr1 63229165 63309823 - 0 0 +NM_146277_Olfr1412 chr1 94484843 94486082 + 0 0 +NM_146305_Olfr420 chr1 176088784 176089871 + 0 0 +NM_146490_Olfr1411 chr1 94493008 94494065 + 0 0 +NM_146491_Olfr1410 chr1 94504416 94505384 + 0 0 +NM_146715_Olfr419 chr1 176180115 176200418 - 0 0 +NM_146716_Olfr432 chr1 175977437 175981444 + 0 0 +NM_146717_Olfr433 chr1 175971174 175973629 + 0 0 +NM_146718_Olfr430 chr1 175999350 176000384 + 0 0 +NM_146720_Olfr421 chr1 176072364 176082596 + 0 0 +NM_146721_Olfr424 chr1 176057388 176067824 + 0 0 +NM_146722_Olfr429 chr1 176019173 176020111 + 0 0 +NM_146761_Olfr414 chr1 176360513 176361670 + 0 0 +NM_146764_Olfr1408 chr1 175060414 175083388 - 0 0 +NM_146881_Olfr1404 chr1 175145784 175146725 + 0 0 +NM_147037_Olfr1413 chr1 94469750 94470721 + 0 0 +NM_148937_Plcd4 chr1 74589462 74614368 + 0 0 +NM_152895_Kdm5b chr1 136455975 136529487 + 0 0 +NM_152915_Dner chr1 84366415 84706993 - 0 0 +NM_153064_Ndufs2 chr1 173164989 173180188 - 0 0 +NM_153088_Ctdsp1 chr1 74438065 74443852 + 0 0 +NM_153111_Fev chr1 74915158 74932371 - 0 0 +NM_153114_Otos chr1 94540797 94553072 - 0 0 +NM_153137_Traf3ip3 chr1 195001656 195027877 - 0 0 +NM_153154_Tcfap2d chr1 19027377 19157044 + 0 0 +NM_153171_Rgs13 chr1 145985803 146024550 - 0 0 +NM_153179_Pkhd1 chr1 20040166 20661582 - 0 0 +NM_153408_Neurl3 chr1 36321504 36355139 - 0 0 +NM_153502_Ankrd23 chr1 36587038 36593708 - 0 0 +NM_153530_Dis3l2 chr1 88570607 88946671 + 0 0 +NM_153539_Fam5c chr1 148341910 148749599 + 0 0 +NM_153555_Wdr42a chr1 174078166 174127554 + 0 0 +NM_153556_Pms1 chr1 53245508 53353841 - 0 0 +NM_153601_Lgsn chr1 31221394 31261688 + 0 0 +NM_153744_Prkag3 chr1 74785516 74825109 - 0 0 +NM_153774_Ipo9 chr1 137278207 137330146 - 0 0 +NM_170597_Creg2 chr1 39677083 39708307 - 0 0 +NM_170755_Fam134a chr1 75137484 75144869 + 0 0 +NM_172054_Txndc9 chr1 38041434 38054101 - 0 0 +NM_172124_B3gat2 chr1 23755411 23855977 + 0 0 +NM_172294_Sulf1 chr1 12708560 12851249 + 0 0 +NM_172406_Trak2 chr1 58955979 59031177 - 0 0 +NM_172422_Fastkd2 chr1 63777134 63803028 + 0 0 +NM_172430_Sphkap chr1 83207585 83404745 - 0 0 +NM_172463_Sned1 chr1 95132418 95197642 + 0 0 +NM_172484_E030049G20Rik chr1 127810213 128389504 - 0 0 +NM_172485_Thsd7b chr1 131169889 132172070 + 0 0 +NM_172499_Mfsd9 chr1 40828883 40921070 - 0 0 +NM_172510_Mfsd4 chr1 133919383 133964629 - 0 0 +NM_172513_Fam126b chr1 58575029 58643157 - 0 0 +NM_172516_Dstyk chr1 134314046 134363525 + 0 0 +NM_172517_Rbbp5 chr1 134368568 134402423 + 0 0 +NM_172643_Zbtb41 chr1 141318960 141349577 + 0 0 +NM_172644_Dars2 chr1 162970732 163001279 - 0 0 +NM_172647_F11r chr1 173365700 173394971 + 0 0 +NM_172648_Ifi205 chr1 175664572 175958593 - 0 0 +NM_172650_Kctd3 chr1 190794974 190831710 - 0 0 +NM_172652_4632411B12Rik chr1 36381585 36426026 - 0 0 +NM_172653_Slc39a10 chr1 46863572 46949677 - 0 0 +NM_172656_Stradb chr1 59012025 59052817 + 0 0 +NM_172841_Slco5a1 chr1 12857471 12982812 - 0 0 +NM_172843_Tor1aip2 chr1 157906541 157915942 + 0 0 +NM_172844_Fmo9 chr1 168589849 168611976 - 0 0 +NM_172845_Adamts4 chr1 173178880 173192383 + 0 0 +NM_172846_Dnahc14 chr1 183669052 183694102 + 0 0 +NM_172850_Ankmy1 chr1 94757771 94799473 - 0 0 +NM_172851_Cntnap5b chr1 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 +NM_175031_Stk36 chr1 74648039 74683468 + 0 0 +NM_175106_Tmem177 chr1 121793019 121809709 - 0 0 +NM_175118_Dusp28 chr1 94803563 94805012 + 0 0 +NM_175127_Fbxo28 chr1 184242976 184303818 - 0 0 +NM_175170_Pogk chr1 168314763 168391350 - 0 0 +NM_175200_Als2cr11 chr1 59053967 59151744 - 0 0 +NM_175210_Abca12 chr1 71207671 71501632 - 0 0 +NM_175236_Adhfe1 chr1 9538049 9570746 + 0 0 +NM_175259_Shisa4 chr1 137267654 137274885 - 0 0 +NM_175293_D630023F18Rik chr1 65151863 65176420 - 0 0 +NM_175294_Nucks1 chr1 133807079 133832888 + 0 0 +NM_175296_Mael chr1 168115771 168178081 - 0 0 +NM_175370_Als2cr12 chr1 58714975 58752801 - 0 0 +NM_175382_2700049P18Rik chr1 133344141 133436449 + 0 0 +NM_175439_Mars2 chr1 55294084 55297625 + 0 0 +NM_175443_Etnk2 chr1 135260167 135276893 + 0 0 +NM_175460_Nmnat2 chr1 154802128 154966391 + 0 0 +NM_175461_Fam78b chr1 168898096 169021408 + 0 0 +NM_175564_Tmem169 chr1 72330953 72349677 + 0 0 +NM_175642_Bai3 chr1 25084207 25887514 - 0 0 +NM_175686_Prrx1 chr1 165175252 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 +NM_177756_Glt25d2 chr1 154223175 154357825 + 0 0 +NM_177757_Kif26b chr1 180720593 180862983 + 0 0 +NM_177781_Trpa1 chr1 14861962 14909072 - 0 0 +NM_177834_Cpa6 chr1 10314801 10710026 - 0 0 +NM_177838_Fam163a chr1 157923096 158135544 - 0 0 +NM_177839_Tnn chr1 161966935 162084477 - 0 0 +NM_178051_Mterfd2 chr1 95195779 95202630 - 0 0 +NM_178055_Dnajb2 chr1 75233016 75242264 + 0 0 +NM_178119_Agap1 chr1 91351421 91791845 + 0 0 +NM_178241_Il8ra chr1 74238380 74241205 - 0 0 +NM_178243_5830403L16Rik chr1 155697272 155747352 - 0 0 +NM_178244_Teddm1 chr1 155724147 155740188 + 0 0 +NM_178399_3110035E14Rik chr1 9591248 9617222 + 0 0 +NM_178405_Atp1a2 chr1 174201852 174233438 - 0 0 +NM_178593_Rcsd1 chr1 167572007 167639868 - 0 0 +NM_178598_Tagln2 chr1 174430123 174475991 + 0 0 +NM_178601_Imp4 chr1 34496377 34511555 + 0 0 +NM_178632_Ints7 chr1 193399085 193447550 + 0 0 +NM_178653_Sccpdh chr1 181598088 181617593 + 0 0 +NM_178690_Rab3gap1 chr1 129765355 129840723 + 0 0 +NM_178691_Yod1 chr1 132612680 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
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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 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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 . . . . . . . . .
--- /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): +# +#<UniqueID> <Build> <Description> <PathToGeneListFile> +# +#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. +
--- /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 @@ +<tables> + <table name="rnachipintegrator_canonical_genes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/rnachipintegrator_canonical_genes.loc" /> + </table> +</tables>
--- /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 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="python_xlwt" version="0.7.5"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/x/xlwt/xlwt-0.7.5.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Installs Python module xlwt 0.7.5</readme> + </package> + <package name="python_xlrd" version="0.9.3"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/x/xlrd/xlrd-0.9.3.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Installs Python module xlrd 0.9.3</readme> + </package> + <package name="python_xlutils" version="1.7.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://pypi.python.org/packages/source/x/xlutils/xlutils-1.7.1.tar.gz</action> + <action type="make_directory">$INSTALL_DIR/lib/python</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme>Installs Python module xlutils 1.7.1</readme> + </package> + <package name="rnachipintegrator" version="0.4.4"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://github.com/fls-bioinformatics-core/RnaChipIntegrator/archive/v0.4.4.tar.gz</action> + <action type="move_file"> + <source>RnaChipIntegrator.py</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>Spreadsheet.py</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme>Installs RnaChipIntegrator 0.4.3</readme> + </package> +</tool_dependency>