| Previous changeset 0:d9c1f2133124 (2015-06-30) Next changeset 2:dc498b03ca9a (2016-09-01) |
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Commit message:
Uploaded version 1.0.0.0. |
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modified:
README.rst rnachipintegrator_canonical_genes.xml rnachipintegrator_macros.xml rnachipintegrator_wrapper.sh rnachipintegrator_wrapper.xml test-data/mm9_peaks.xls tool_dependencies.xml |
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added:
test-data/features.txt test-data/features_per_peak1.out test-data/features_per_peak2.out test-data/features_per_peak3.out test-data/features_per_peak4.out test-data/features_per_peak4.summary test-data/features_per_summit.out test-data/mm9_features_per_peak.out test-data/mm9_features_per_peak1.out test-data/mm9_features_per_peak3.out test-data/mm9_features_per_peak3.summary test-data/mm9_features_per_peak_compact.out test-data/mm9_features_per_summit.out test-data/mm9_peaks1.xlsx test-data/mm9_peaks3.xlsx test-data/mm9_peaks_compact.xls test-data/mm9_peaks_per_feature.out test-data/mm9_peaks_per_feature1.out test-data/mm9_peaks_per_feature3.out test-data/mm9_peaks_per_feature3.summary test-data/mm9_peaks_per_feature_compact.out test-data/mm9_summits.xlsx test-data/mm9_summits_per_feature.out test-data/peaks.txt test-data/peaks1.xlsx test-data/peaks2.xlsx test-data/peaks3.xlsx test-data/peaks4.xlsx test-data/peaks_per_feature1.out test-data/peaks_per_feature2.out test-data/peaks_per_feature3.out test-data/peaks_per_feature4.out test-data/peaks_per_feature4.summary test-data/summits.txt test-data/summits.xlsx test-data/summits_per_feature.out |
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removed:
test-data/ChIP_peaks.txt test-data/ChIP_summits.txt test-data/ExpressionData.txt test-data/mm9_summits.xls test-data/mm9_summits_to_transcripts.out test-data/mm9_transcripts_to_edges.out test-data/mm9_transcripts_to_edges.summary test-data/mm9_tss_to_edges.out test-data/mm9_tss_to_edges.summary test-data/mm9_tss_to_summits.out test-data/peaks.xls test-data/peaks_to_transcripts.out test-data/summits.xls test-data/transcripts_to_edges.out test-data/transcripts_to_edges.summary test-data/tss_to_edges.out test-data/tss_to_edges.summary test-data/tss_to_summits.out |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 README.rst --- a/README.rst Tue Jun 30 06:44:06 2015 -0400 +++ b/README.rst Wed Feb 24 09:39:14 2016 -0500 |
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| @@ -90,12 +90,10 @@ 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: +To enable Excel (XLS) 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". + <datatype extension="xlsx" type="galaxy.datatypes.binary:Binary" mimetype="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"/> Restarting Galaxy should mean that the browser correctly handles Excel outputs from RnaChipIntegrator. @@ -106,6 +104,11 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +1.0.0.0 - Update to use latest ``RnaChipIntegrator`` version 1.0.0. +0.5.0-0 - Significant update to bring tools in line with + ``RnaChipIntegrator`` version 0.5.0, including removing the + distinction between 'regions' and 'summits' for input peaks, + and otherwise attempting to simplify the tools for users. 0.4.4-0 - Initial version pushed to toolshed ========== ====================================================================== |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 rnachipintegrator_canonical_genes.xml --- a/rnachipintegrator_canonical_genes.xml Tue Jun 30 06:44:06 2015 -0400 +++ b/rnachipintegrator_canonical_genes.xml Wed Feb 24 09:39:14 2016 -0500 |
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| b'@@ -1,153 +1,111 @@\n-<tool id="rnachipintegrator_canonical_genes" name="Analyse canonical genes against ChIP data" version="@VERSION@-0">\n+<tool id="rnachipintegrator_canonical_genes" name="Analyse canonical genes against \'peak\' data" version="@VERSION@.0">\n <description>using RnaChipIntegrator</description>\n <macros>\n <import>rnachipintegrator_macros.xml</import>\n </macros>\n <expand macro="requirements" />\n <expand macro="version_command" />\n- <command interpreter="bash">rnachipintegrator_wrapper.sh\n- #if str( $analysis_options.peak_type ) == "summits"\n- #if str( $analysis_options.window ) != ""\n- --window=$analysis_options.window\n- #end if\n- #if str( $analysis_options.cutoff ) != ""\n- --cutoff=$analysis_options.cutoff\n- #end if\n+ <command interpreter="bash"><![CDATA[\n+ rnachipintegrator_wrapper.sh\n+ #if $peaks_in.metadata.chromCol\n+ --peak_cols=${peaks_in.metadata.chromCol},${peaks_in.metadata.startCol},${peaks_in.metadata.endCol}\n+ #end if\n+ #if str( $cutoff ) != ""\n+ --cutoff=$cutoff\n+ #else\n+ --cutoff=0\n #end if\n- #if str( $analysis_options.peak_type ) == "regions"\n- #if str( $analysis_options.edge_cutoff ) != ""\n- --edge-cutoff=$analysis_options.edge_cutoff\n- #end if\n- #if str( $analysis_options.number ) != ""\n- --number=$analysis_options.number\n- #end if\n- #if (str( $analysis_options.promoter_start ) != "" and str( $analysis_options.promoter_end ))\n- --promoter_region=$analysis_options.promoter_start,$analysis_options.promoter_end\n+ #if str( $number ) != ""\n+ --number=$number\n+ #end if\n+ --promoter_region=$promoter_start,$promoter_end\n+ --edge=$edge\n+ --xlsx_file "$xlsx_out"\n+ --output_files "$peaks_per_feature_out" "$features_per_peak_out"\n+ #if $output.compact_format\n+ --compact\n+ #else\n+ #if $output.summary\n+ --summary_files "$peaks_per_feature_summary" "$features_per_peak_summary"\n #end if\n- #if $analysis_options.pad_output\n- --pad\n- #end if\n+ ${output.pad_output}\n #end if\n- ${canonical_genes.fields.path} $chipseq\n- --output_xls $xls_output\n- #if $results_as_zip\n- --zip_file $zip_file\n- #else\n- #if str( $analysis_options.peak_type ) == "summits"\n- --summit_outputs $peaks_to_transcripts_out $tss_to_summits_out\n- #end if\n- #if str( $analysis_options.peak_type ) == "regions"\n- --peak_outputs $transcripts_to_edges_out\n- $transcripts_to_edges_summary\n- $tss_to_edges_out\n- $tss_to_edges_summary\n- #end if\n- #end if\n- </command>\n+ "${canonical_genes.fields.path}" "$peaks_in"\n+ ]]></command>\n <inputs>\n- <param format="tabular" name="chipseq" type="data" label="ChIP peaks data file" />\n- <param name="canonical_genes" type="select" label="Canonical genes to analyse ChIP peaks against">\n+ <param format="tabular" name="peaks_in" type="data" label="Peaks" />\n+ <param name="canonical_genes" type="select" label="Canonical genes to analyse peaks against">\n <options from_data_table="rnachipintegrator_canonical_genes">\n </options>\n </param>\n- <conditional name="analysis_options">\n- <!-- user must specify if ChIP peaks are summits or regions -->\n- <param name="peak_type" type="select" label="ChIP peaks are"\n-\t help="Options and outputs depend on whether ChIP data are summits or regions">\n- <option value="summits">summits</option>\n- <option value="regions">regions</option>\n- </param>\n- <when value="summits">\n- <param name="window" type="integer" value="20000" optional="true"\n-\t label="Maximum distance a peak can be from each transcript\n-\t\t TSS before being omitted from analysis" />\n- <param name="cutoff" type="integer" value="130000" optional="true"\n-\t label="Maximum distance a transcript TSS can be from each\n-\t\t peak before being omitted from the analysis" />\n- </when>\n- <when value="regions">\n- <param name="edge_cutoff" type="integer" value="10000" opt'..b'peak (one per line):\n+The peak data must be in a tabular file with at least 3 columns of data\n+for each peak (one peak per line):\n \n-====== ========== ======================================================================\n+====== ========== =================================\n Column Name Description\n-====== ========== ======================================================================\n- 1 chr Chromosome name (must match one of those in expression data file)\n- 2 start Start position of the peak \n- 3 end End position of the peak (start + 1 for summit data)\n-====== ========== ======================================================================\n-\n-The ChIP peak data can be either the summit (in which case \'end\' - \'start\' = 1) or the\n-entire extent of the binding region (with \'start\' and \'end\' indicating the limits).\n+====== ========== =================================\n+ 1 chr Chromosome name\n+ 2 start Start position of the peak\n+ 3 end End position of the peak\n+====== ========== =================================\n \n -------------\n \n .. class:: infomark\n \n-**Output**\n+**Outputs**\n+\n+The key outputs from the tool are two lists compromising the nearest\n+peaks for each gene, and the nearest gene for each peak (one\n+dataset for each list).\n+\n+There are two formats for reporting: "compact" and "full":\n \n-The outputs from this tool vary depending on the type of ChIP data that is input (i.e\n-summits or peaks), however generally there is one tab-delimited results file for each\n-analysis described above in the **What it does** section (some analyses output a second\n-file with just the "best" hits).\n+ * **Compact output** reports all the hits for each peak or gene on\n+ a single line of output;\n+ * **Full output** reports each peak/gene pair on a separate line\n+ (i.e. a multi-line output format).\n+\n+In "full" output mode, additional options are available:\n+\n+ * The output files can be "padded" with extra (empty) lines to ensure\n+ that there are always the same number of lines for each peak or\n+ gene, if fewer than the requested number of hits are found.\n+ * "Summary" datasets can also be requested, which include just the\n+ nearest peak reported for each gene (and vice versa).\n \n-A history item will be generated for each output file, unless the option to put them\n-into a single zip archive is selected; this archive file will have to be downloaded\n-and unzipped on your local machine. It is recommended that you refer to the\n-RnaChipIntegrator documentation for information on the contents of each output file:\n-https://github.com/fls-bioinformatics-core/RnaChipIntegrator/blob/master/doc/MANUAL.markdown\n+In either mode these data will also be output in a single MS Excel file,\n+which contains one sheet per result set.\n+\n+.. class:: warning\n+\n+Using "compact" output with the number of hits limited to more than 4\n+peak/gene pairs (or with no limit at all) can result in a large number\n+of columns in the output files, which in some versions of Galaxy will\n+not be properly displayed. However the data files themselves should be\n+okay.\n \n-In addition an Excel spreadsheet (with one page for each analysis performed) is always\n-produced.\n+-------------\n+\n+.. class:: informark\n+\n+**More information**\n+\n+It is recommended that you refer to the ``RnaChipIntegrator``\n+documentation for information on the contents of each output file:\n+\n+* http://rnachipintegrator.readthedocs.org/en/latest/\n \n -------------\n \n@@ -228,8 +194,9 @@\n This Galaxy tool has been developed within the Bioinformatics Core Facility at the\n University of Manchester. It runs the RnaChipIntegrator package which has also been\n developed by this group, and is documented at\n-http://fls-bioinformatics-core.github.com/RnaChipIntegrator/\n+https://pypi.python.org/pypi/RnaChipIntegrator/\n \n Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.\n </help>\n+ <expand macro="citations" />\n </tool>\n' |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 rnachipintegrator_macros.xml --- a/rnachipintegrator_macros.xml Tue Jun 30 06:44:06 2015 -0400 +++ b/rnachipintegrator_macros.xml Wed Feb 24 09:39:14 2016 -0500 |
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| @@ -1,14 +1,68 @@ <macros> - <token name="@VERSION@">0.4.4</token> + <token name="@VERSION@">1.0.0</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> + <requirement type="package" version="0.8.4">python_xlsxwriter</requirement> + <requirement type="package" version="1.0.0">rnachipintegrator</requirement> </requirements> </xml> <xml name="version_command"> - <version_command>rnachipintegrator --version</version_command> - </xml> + <version_command>RnaChipIntegrator --version</version_command> + </xml> + <xml name="analysis_options"> + <param name="cutoff" type="integer" value="1000000" optional="true" + label="Maximum distance between a gene/peak pair + before it is omitted from the analyses (bp)" + help="Leave blank for no limit (--cutoff)" /> + <param name="number" type="integer" value="4" optional="true" + label="Maximum number of gene/peak pairs to report from + the analyses" + help="Leave blank for no limit (--number)" /> + <param name="promoter_start" type="integer" value="-1000" optional="true" + label="Start of promoter region with respect to gene TSS" /> + <param name="promoter_end" type="integer" value="100" optional="true" + label="End of promoter region with respect to gene TSS" /> + <param name="edge" type="select" + label="Gene 'edges' to consider in distance calculations" + help="(--edge)"> + <option value="tss" selected="true">TSS only</option> + <option value="both">Nearest of TSS or TES</option> + </param> + </xml> + <xml name="output_options"> + <conditional name="output"> + <param name="compact_format" type="boolean" checked="true" + truevalue="true" falsevalue="false" + label="Use 'compact' output format" + help="Puts all hits for each peak or gene on a single line + (--compact)" /> + <when value="true"> + </when> + <when value="false"> + <param name="pad_output" type="boolean" checked="false" + truevalue="--pad" falsevalue="" + 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)" /> + <param name="summary" type="boolean" checked="false" + truevalue="true" falsevalue="false" + label="Output additional 'summary' datasets" + help="Summaries contain only the top hits for each peak + or feature (--summary)" /> + </when> + </conditional> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex">@misc{Briggs2016, + author = {Briggs PJ, Donaldson IJ, Zeef LAH}, + title = {RnaChipIntegrator}, + publisher = {GitHub}, + journal = {GitHub repository}, + year = {2016}, + howpublished = {\url{https://github.com/fls-bioinformatics-core/RnaChipIntegrator}}, + version = {1.0.0} +}</citation> + </citations> + </xml> </macros> |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 rnachipintegrator_wrapper.sh --- a/rnachipintegrator_wrapper.sh Tue Jun 30 06:44:06 2015 -0400 +++ b/rnachipintegrator_wrapper.sh Wed Feb 24 09:39:14 2016 -0500 |
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| @@ -4,27 +4,30 @@ # # usage: sh rnachipintegrator_wrapper.sh [OPTIONS] <rnaseq_in> <chipseq_in> --output_xls <xls_out> # -echo RnaChipIntegrator: analyse gene expression and ChIP data +echo RnaChipIntegrator: analyse gene and peak data # # Collect command line options opts= -output_xls= -peaks_to_transcripts_out= +xlsx_file= zip_file= +gene_centric= +peak_centric= +gene_centric_summary= +peak_centric_summary= while [ ! -z "$1" ] ; do case $1 in - --output_xls) - shift; output_xls=$1 + --xlsx_file) + shift; xlsx_file=$1 + opts="$opts --xlsx" ;; - --summit_outputs) - shift; peaks_to_transcripts_out=$1 - shift; tss_to_summits_out=$1 + --output_files) + shift; gene_centric=$1 + shift; peak_centric=$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 + --summary_files) + shift; gene_centric_summary=$1 + shift; peak_centric_summary=$1 + opts="$opts --summary" ;; --zip_file) shift; zip_file=$1 @@ -39,9 +42,9 @@ # Run RnaChipIntegrator # NB append stderr to stdout otherwise Galaxy job will fail # Direct output to a temporary directory -outdir=`mktemp -d` +outdir=$(mktemp -d) base_name=galaxy -cmd="RnaChipIntegrator.py --project=${outdir}/${base_name} $opts" +cmd="RnaChipIntegrator --name=${outdir}/${base_name} $opts" echo $cmd $cmd 2>&1 # @@ -54,19 +57,23 @@ exit $exit_status fi # -# Deal with output files - XLS -if [ -f "${outdir}/${base_name}.xls" ] ; then - /bin/mv ${outdir}/${base_name}.xls $output_xls +# Deal with output XLSX file +if [ -f "${outdir}/${base_name}.xlsx" ] ; then + /bin/mv ${outdir}/${base_name}.xlsx $xlsx_file else - echo No file ${outdir}/${base_name}.xls >&2 + echo No file ${outdir}/${base_name}.xlsx >&2 # Clean up and exit /bin/rm -rf $outdir exit 1 fi # -# Zip file +# Generate zip file if [ ! -z "$zip_file" ] ; then - for ext in "PeaksToTranscripts" "TSSToSummits" "TranscriptsToPeakEdges" "TranscriptsToPeakEdges_summary" "TSSToPeakEdges" "TSSToPeakEdges_summary" ; do + for ext in \ + gene_centric \ + gene_centric_summary \ + peak_centric \ + peak_centric_summary ; do txt_file=${outdir}/${base_name}_${ext}.txt if [ -f "$txt_file" ] ; then zip -j -g ${outdir}/archive.zip $txt_file @@ -75,61 +82,22 @@ /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 $outfile >&2 +# Collect tab delimited files +for ext in \ + gene_centric \ + gene_centric_summary \ + peak_centric \ + peak_centric_summary ; do + eval dest=\$$ext + if [ ! -z "$dest" ] ; then + outfile=${outdir}/${base_name}_${ext}.txt + if [ -f "$outfile" ] ; then + /bin/mv $outfile $dest + else + echo ERROR missing output file $outfile >&2 + fi fi -fi -if [ ! -z "$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 +done # # Clean up /bin/rm -rf $outdir |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 rnachipintegrator_wrapper.xml --- a/rnachipintegrator_wrapper.xml Tue Jun 30 06:44:06 2015 -0400 +++ b/rnachipintegrator_wrapper.xml Wed Feb 24 09:39:14 2016 -0500 |
| [ |
| b'@@ -1,161 +1,150 @@\n <?xml version="1.0" encoding="utf-8"?>\n-<tool id="rnachipintegrator_wrapper" name="RnaChipIntegrator" version="@VERSION@-0">\n- <description>Integrated analysis of gene expression data and ChIP data</description>\n+<tool id="rnachipintegrator_wrapper" name="RnaChipIntegrator" version="@VERSION@.0">\n+ <description>Integrated analysis of \'gene\' and \'peak\' data</description>\n <macros>\n <import>rnachipintegrator_macros.xml</import>\n </macros>\n <expand macro="requirements" />\n <expand macro="version_command" />\n- <command interpreter="bash">rnachipintegrator_wrapper.sh\n- #if str( $analysis_options.peak_type ) == "summits"\n- #if str( $analysis_options.window ) != ""\n- --window=$analysis_options.window\n- #end if\n- #if str( $analysis_options.cutoff ) != ""\n- --cutoff=$analysis_options.cutoff\n- #end if\n+ <command interpreter="bash"><![CDATA[\n+ rnachipintegrator_wrapper.sh\n+ #if $peaks_in.metadata.chromCol\n+ --peak_cols=${peaks_in.metadata.chromCol},${peaks_in.metadata.startCol},${peaks_in.metadata.endCol}\n #end if\n- #if str( $analysis_options.peak_type ) == "regions"\n- #if str( $analysis_options.edge_cutoff ) != ""\n- --edge-cutoff=$analysis_options.edge_cutoff\n- #end if\n- #if str( $analysis_options.number ) != ""\n- --number=$analysis_options.number\n- #end if\n- #if (str( $analysis_options.promoter_start ) != "" and str( $analysis_options.promoter_end ))\n- --promoter_region=$analysis_options.promoter_start,$analysis_options.promoter_end\n- #end if\n- #if $analysis_options.pad_output\n- --pad\n- #end if\n+ #if str( $cutoff ) != ""\n+ --cutoff=$cutoff\n+ #else\n+ --cutoff=0\n #end if\n- $rnaseq $chipseq\n- --output_xls $xls_output\n- #if $results_as_zip\n- --zip_file $zip_file\n- #else\n- #if str( $analysis_options.peak_type ) == "summits"\n- --summit_outputs $peaks_to_transcripts_out $tss_to_summits_out\n- #end if\n- #if str( $analysis_options.peak_type ) == "regions"\n- --peak_outputs $transcripts_to_edges_out\n- $transcripts_to_edges_summary\n- $tss_to_edges_out\n- $tss_to_edges_summary\n- #end if\n+ #if str( $number ) != ""\n+ --number=$number\n #end if\n- </command>\n+ --promoter_region=$promoter_start,$promoter_end\n+ --edge=$edge\n+ $diff_expressed_only\n+ --xlsx_file "$xlsx_out"\n+ --output_files "$peaks_per_feature_out" "$features_per_peak_out"\n+ #if $output.compact_format\n+ --compact\n+ #else\n+ #if $output.summary\n+ --summary_files "$peaks_per_feature_summary" "$features_per_peak_summary"\n+ #end if\n+ ${output.pad_output}\n+ #end if\n+ "$features_in" "$peaks_in"\n+ ]]></command>\n <inputs>\n- <param format="tabular" name="rnaseq" type="data" label="Gene expression data file" />\n- <param format="tabular" name="chipseq" type="data" label="ChIP peaks data file" />\n- <conditional name="analysis_options">\n- <!-- user must specify if ChIP peaks are summits or regions -->\n- <param name="peak_type" type="select" label="ChIP peaks are"\n-\t help="Options and outputs depend on whether ChIP data are summits or regions">\n- <option value="summits">summits</option>\n- <option value="regions">regions</option>\n- </param>\n- <when value="summits">\n- <param name="window" type="integer" value="20000" optional="true"\n-\t label="Maximum distance a peak can be from each transcript\n-\t\t TSS before being omitted from analysis" />\n- <param name="cutoff" type="integer" value="130000" optional="true"\n-\t label="Maximum distance a transcript TSS can be from each\n-\t\t peak before being omitted from the analysis" />\n- </when>\n- <when value="regions">\n- <param name="edge_cutoff" type="integer" value="10000" optional="true"\n-\t label="Maximum distance a transcript edge can be from the\n-\t\t peak edge before being omitted from the analysis"\n-\t help="Set to zero to indicate that no cut off should be applied" />\n- '..b'tional: indicates gene is differentially expressed (1) or not (0)\n ====== ========== ======================================================================\n \n-The ChIP-seq data must be in a tab-delimited file with 3 columns of data for each\n-ChIP peak (one per line):\n+The peak data must be in a tabular file with at least 3 columns of data\n+for each peak (one peak per line):\n \n-====== ========== ======================================================================\n+====== ========== =================================\n Column Name Description\n-====== ========== ======================================================================\n- 1 chr Chromosome name (must match one of those in expression data file)\n+====== ========== =================================\n+ 1 chr Chromosome name\n 2 start Start position of the peak \n- 3 end End position of the peak (start + 1 for summit data)\n-====== ========== ======================================================================\n+ 3 end End position of the peak\n+====== ========== =================================\n \n-The ChIP peak data can be either the summit (in which case \'end\' - \'start\' = 1) or the\n-entire extent of the binding region (with \'start\' and \'end\' indicating the limits).\n+If peak data is in ``bed`` format then the tool will automatically\n+assign the correct columns, otherwise the first three columns of data\n+will be used.\n \n -------------\n \n .. class:: infomark\n \n-**Output**\n+**Outputs**\n+\n+The key outputs from the tool are two lists compromising the nearest\n+peaks for each gene, and the nearest gene for each peak (one dataset\n+for each list).\n+\n+There are two formats for reporting: "compact" and "full":\n \n-The outputs from this tool vary depending on the type of data that is input, however\n-generally there is one tab-delimited results file for each analysis described above\n-in the **What it does** section (some analyses output a second file with just the\n-"best" hits).\n+ * **Compact output** reports all the hits for each peak or gene on\n+ a single line of output;\n+ * **Full output** reports each peak/gene pair on a separate line\n+ (i.e. a multi-line output format).\n+\n+In "full" output mode, additional options are available:\n+\n+ * The output files can be "padded" with extra (empty) lines to ensure\n+ that there are always the same number of lines for each peak or\n+ gene, if fewer than the requested number of hits are found.\n+ * "Summary" datasets can also be requested, which include just the\n+ nearest peak reported for each gene (and vice versa).\n \n-A history item will be generated for each output file, unless the option to put them\n-into a single zip archive is selected; this archive file will have to be downloaded\n-and unzipped on your local machine. It is recommended that you refer to the\n-RnaChipIntegrator documentation for information on the contents of each output file:\n-https://github.com/fls-bioinformatics-core/RnaChipIntegrator/blob/master/doc/MANUAL.markdown\n+In either mode these data will also be output in a single MS Excel file,\n+which contains one sheet per result set.\n+\n+.. class:: warning\n+\n+Using "compact" output with the number of hits limited to more than 4\n+peak/gene pairs (or with no limit at all) can result in a large number\n+of columns in the output files, which in some versions of Galaxy will\n+not be properly displayed. However the data files themselves should be\n+okay.\n \n-In addition an Excel spreadsheet (with one page for each analysis performed) is always\n-produced.\n+-------------\n+\n+.. class:: informark\n+\n+**More information**\n+\n+It is recommended that you refer to the ``RnaChipIntegrator``\n+documentation for information on the contents of each output file:\n+\n+* http://rnachipintegrator.readthedocs.org/en/latest/\n \n -------------\n \n@@ -259,4 +260,5 @@\n \n Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.\n </help>\n+ <expand macro="citations" />\n </tool>\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/ChIP_peaks.txt --- a/test-data/ChIP_peaks.txt Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,70 +0,0 @@ -#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 |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/ChIP_summits.txt --- a/test-data/ChIP_summits.txt Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,654 +0,0 @@\n-#peak\tmid\tplus1\r\n-chr10\t106033584\t106033585\r\n-chr10\t106033751\t106033752\r\n-chr10\t107429926\t107429927\r\n-chr10\t114752719\t114752720\r\n-chr10\t114994096\t114994097\r\n-chr10\t127058840\t127058841\r\n-chr10\t127184557\t127184558\r\n-chr10\t13089536\t13089537\r\n-chr10\t13408622\t13408623\r\n-chr10\t17725474\t17725475\r\n-chr10\t21862583\t21862584\r\n-chr10\t21862774\t21862775\r\n-chr10\t31587625\t31587626\r\n-chr10\t41613298\t41613299\r\n-chr10\t43640892\t43640893\r\n-chr10\t43740181\t43740182\r\n-chr10\t45093322\t45093323\r\n-chr10\t57702300\t57702301\r\n-chr10\t59362596\t59362597\r\n-chr10\t59693654\t59693655\r\n-chr10\t60613588\t60613589\r\n-chr10\t60696228\t60696229\r\n-chr10\t67567003\t67567004\r\n-chr10\t76664902\t76664903\r\n-chr10\t7707698\t7707699\r\n-chr10\t79808095\t79808096\r\n-chr10\t80126390\t80126391\r\n-chr10\t81033719\t81033720\r\n-chr10\t82306942\t82306943\r\n-chr10\t82517145\t82517146\r\n-chr10\t84922053\t84922054\r\n-chr10\t88433836\t88433837\r\n-chr10\t89195191\t89195192\r\n-chr10\t93642365\t93642366\r\n-chr10\t94183365\t94183366\r\n-chr10\t94306306\t94306307\r\n-chr1\t10627335\t10627336\r\n-chr1\t108757655\t108757656\r\n-chr11\t100148455\t100148456\r\n-chr11\t100964551\t100964552\r\n-chr11\t102973374\t102973375\r\n-chr11\t103196320\t103196321\r\n-chr11\t107278688\t107278689\r\n-chr11\t110241161\t110241162\r\n-chr11\t114563829\t114563830\r\n-chr11\t115639021\t115639022\r\n-chr11\t115836265\t115836266\r\n-chr11\t119827740\t119827741\r\n-chr11\t120952392\t120952393\r\n-chr11\t121341339\t121341340\r\n-chr11\t16560450\t16560451\r\n-chr11\t18798190\t18798191\r\n-chr11\t19003164\t19003165\r\n-chr11\t20247624\t20247625\r\n-chr1\t120770337\t120770338\r\n-chr11\t21483462\t21483463\r\n-chr11\t29514477\t29514478\r\n-chr11\t3000481\t3000482\r\n-chr11\t3266659\t3266660\r\n-chr1\t132961088\t132961089\r\n-chr1\t133124938\t133124939\r\n-chr11\t34495361\t34495362\r\n-chr1\t135592753\t135592754\r\n-chr1\t135862036\t135862037\r\n-chr1\t136966533\t136966534\r\n-chr1\t13839396\t13839397\r\n-chr1\t138447793\t138447794\r\n-chr1\t140391721\t140391722\r\n-chr11\t4116866\t4116867\r\n-chr1\t145601109\t145601110\r\n-chr11\t50300699\t50300700\r\n-chr11\t5481053\t5481054\r\n-chr1\t154981623\t154981624\r\n-chr1\t155133374\t155133375\r\n-chr1\t158520668\t158520669\r\n-chr1\t158547339\t158547340\r\n-chr1\t158590699\t158590700\r\n-chr1\t158845321\t158845322\r\n-chr1\t159250801\t159250802\r\n-chr11\t59272503\t59272504\r\n-chr11\t6069204\t6069205\r\n-chr1\t163837980\t163837981\r\n-chr1\t164225779\t164225780\r\n-chr1\t167233113\t167233114\r\n-chr1\t167916419\t167916420\r\n-chr11\t69572437\t69572438\r\n-chr1\t170265171\t170265172\r\n-chr11\t70397406\t70397407\r\n-chr1\t17040475\t17040476\r\n-chr1\t172630846\t172630847\r\n-chr1\t172630999\t172631000\r\n-chr1\t174386565\t174386566\r\n-chr11\t76126479\t76126480\r\n-chr1\t181071373\t181071374\r\n-chr1\t182489776\t182489777\r\n-chr11\t83860977\t83860978\r\n-chr11\t84381942\t84381943\r\n-chr11\t8483612\t8483613\r\n-chr11\t8541945\t8541946\r\n-chr1\t185865026\t185865027\r\n-chr11\t87257043\t87257044\r\n-chr11\t87967409\t87967410\r\n-chr11\t87967599\t87967600\r\n-chr11\t93986729\t93986730\r\n-chr1\t194268840\t194268841\r\n-chr1\t194655297\t194655298\r\n-chr1\t194967560\t194967561\r\n-chr1\t195334592\t195334593\r\n-chr1\t195340816\t195340817\r\n-chr1\t195348466\t195348467\r\n-chr1\t195352857\t195352858\r\n-chr1\t195394981\t195394982\r\n-chr1\t197067820\t197067821\r\n-chr11\t97171690\t97171691\r\n-chr11\t97233548\t97233549\r\n-chr11\t97297212\t97297213\r\n-chr12\t104299157\t104299158\r\n-chr12\t106237696\t106237697\r\n-chr12\t106674392\t106674393\r\n-chr12\t112330425\t112330426\r\n-chr12\t112477144\t112477145\r\n-chr12\t112975712\t112975713\r\n-chr12\t113981451\t113981452\r\n-chr12\t114119343\t114119344\r\n-chr12\t117853390\t117853391\r\n-chr12\t25562241\t25562242\r\n-chr12\t25648378\t25648379\r\n-chr12\t37211753\t37211754\r\n-chr1\t24619593\t24619594\r\n-chr1\t24619958\t24619959\r\n-chr1\t24741037\t24741038\r\n-chr12\t57923295\t57923296\r\n-chr12\t58725309\t58725310\r\n-chr1\t26744340\t26744341\r\n-chr12\t70755181\t70755182\r\n-chr12\t72971895\t72971896\r\n-chr12\t80608252\t80608253\r\n-chr12\t86926811\t86926812\r\n-chr12\t92932316\t92932317\r\n-chr12\t92984595\t92984596\r\n-chr13\t10082361\t10082362\r\n-chr13\t102618599\t102618600\r\n-chr13\t103679464\t103679465\r\n-chr13\t104768206\t104768207\r\n-chr13\t110051416\t110051417\r\n-chr13\t113548696\t113548697\r\n-chr13\t120276594\t120276595\r\n-chr13\t12578010\t12578011\r\n-chr13\t23610160\t23610161\r\n-chr13\t'..b'31\t72564132\r\n-chr5\t73646186\t73646187\r\n-chr5\t87159785\t87159786\r\n-chr5\t90818821\t90818822\r\n-chr5\t99781594\t99781595\r\n-chr6\t100518848\t100518849\r\n-chr6\t103599133\t103599134\r\n-chr6\t113116711\t113116712\r\n-chr6\t121080230\t121080231\r\n-chr6\t127325975\t127325976\r\n-chr6\t127381753\t127381754\r\n-chr6\t127425244\t127425245\r\n-chr6\t128054836\t128054837\r\n-chr6\t128289233\t128289234\r\n-chr6\t128326644\t128326645\r\n-chr6\t128547343\t128547344\r\n-chr6\t134445175\t134445176\r\n-chr6\t134445312\t134445313\r\n-chr6\t143811364\t143811365\r\n-chr6\t146887669\t146887670\r\n-chr6\t147297840\t147297841\r\n-chr6\t17267124\t17267125\r\n-chr6\t33926636\t33926637\r\n-chr6\t37242315\t37242316\r\n-chr6\t47601314\t47601315\r\n-chr6\t49172166\t49172167\r\n-chr6\t51351355\t51351356\r\n-chr6\t56806957\t56806958\r\n-chr6\t67253361\t67253362\r\n-chr6\t76927942\t76927943\r\n-chr6\t83071812\t83071813\r\n-chr6\t83093011\t83093012\r\n-chr6\t86130730\t86130731\r\n-chr6\t87137073\t87137074\r\n-chr6\t87222111\t87222112\r\n-chr6\t94625281\t94625282\r\n-chr7\t104849801\t104849802\r\n-chr7\t117975070\t117975071\r\n-chr7\t119647132\t119647133\r\n-chr7\t119813749\t119813750\r\n-chr7\t120393123\t120393124\r\n-chr7\t120874367\t120874368\r\n-chr7\t123336714\t123336715\r\n-chr7\t125720143\t125720144\r\n-chr7\t126039427\t126039428\r\n-chr7\t127004913\t127004914\r\n-chr7\t128854935\t128854936\r\n-chr7\t128984541\t128984542\r\n-chr7\t134819118\t134819119\r\n-chr7\t135696903\t135696904\r\n-chr7\t137484210\t137484211\r\n-chr7\t137768001\t137768002\r\n-chr7\t138009297\t138009298\r\n-chr7\t138123566\t138123567\r\n-chr7\t138123699\t138123700\r\n-chr7\t139426142\t139426143\r\n-chr7\t146041529\t146041530\r\n-chr7\t147156352\t147156353\r\n-chr7\t148379180\t148379181\r\n-chr7\t148379362\t148379363\r\n-chr7\t148629281\t148629282\r\n-chr7\t150571560\t150571561\r\n-chr7\t152450338\t152450339\r\n-chr7\t152450519\t152450520\r\n-chr7\t16562058\t16562059\r\n-chr7\t16894872\t16894873\r\n-chr7\t17429367\t17429368\r\n-chr7\t20044401\t20044402\r\n-chr7\t26061110\t26061111\r\n-chr7\t26574315\t26574316\r\n-chr7\t28010205\t28010206\r\n-chr7\t30227710\t30227711\r\n-chr7\t30256558\t30256559\r\n-chr7\t35861923\t35861924\r\n-chr7\t56809068\t56809069\r\n-chr7\t87336398\t87336399\r\n-chr7\t88092779\t88092780\r\n-chr7\t89920499\t89920500\r\n-chr8\t10576464\t10576465\r\n-chr8\t107426996\t107426997\r\n-chr8\t109087961\t109087962\r\n-chr8\t109275046\t109275047\r\n-chr8\t109334564\t109334565\r\n-chr8\t113806188\t113806189\r\n-chr8\t119851483\t119851484\r\n-chr8\t121354388\t121354389\r\n-chr8\t129127362\t129127363\r\n-chr8\t129549456\t129549457\r\n-chr8\t13548998\t13548999\r\n-chr8\t13668465\t13668466\r\n-chr8\t14306960\t14306961\r\n-chr8\t17594804\t17594805\r\n-chr8\t19919526\t19919527\r\n-chr8\t19924810\t19924811\r\n-chr8\t22870138\t22870139\r\n-chr8\t23921280\t23921281\r\n-chr8\t24206095\t24206096\r\n-chr8\t34068894\t34068895\r\n-chr8\t37107644\t37107645\r\n-chr8\t4586605\t4586606\r\n-chr8\t70850825\t70850826\r\n-chr8\t71717281\t71717282\r\n-chr8\t73173598\t73173599\r\n-chr8\t73183558\t73183559\r\n-chr8\t73297497\t73297498\r\n-chr8\t81256455\t81256456\r\n-chr8\t86143616\t86143617\r\n-chr8\t87180694\t87180695\r\n-chr8\t88126748\t88126749\r\n-chr8\t93828640\t93828641\r\n-chr8\t97699878\t97699879\r\n-chr9\t100543647\t100543648\r\n-chr9\t103988283\t103988284\r\n-chr9\t106273656\t106273657\r\n-chr9\t107478162\t107478163\r\n-chr9\t108851463\t108851464\r\n-chr9\t110183808\t110183809\r\n-chr9\t111053664\t111053665\r\n-chr9\t116828689\t116828690\r\n-chr9\t118884586\t118884587\r\n-chr9\t120883928\t120883929\r\n-chr9\t123371104\t123371105\r\n-chr9\t13408238\t13408239\r\n-chr9\t14466849\t14466850\r\n-chr9\t14480293\t14480294\r\n-chr9\t24346538\t24346539\r\n-chr9\t3258857\t3258858\r\n-chr9\t42777363\t42777364\r\n-chr9\t43528251\t43528252\r\n-chr9\t43585984\t43585985\r\n-chr9\t44215148\t44215149\r\n-chr9\t44307103\t44307104\r\n-chr9\t54460731\t54460732\r\n-chr9\t66728918\t66728919\r\n-chr9\t66794084\t66794085\r\n-chr9\t67556540\t67556541\r\n-chr9\t70477636\t70477637\r\n-chr9\t72497695\t72497696\r\n-chr9\t72916030\t72916031\r\n-chr9\t74815214\t74815215\r\n-chr9\t75371664\t75371665\r\n-chr9\t8033087\t8033088\r\n-chr9\t8055015\t8055016\r\n-chr9\t83462792\t83462793\r\n-chr9\t86714892\t86714893\r\n-chrX\t109484691\t109484692\r\n-chrX\t137172820\t137172821\r\n-chrX\t139917606\t139917607\r\n-chrX\t140401017\t140401018\r\n-chrX\t163589625\t163589626\r\n-chrX\t166360754\t166360755\r\n-chrX\t166427362\t166427363\r\n-chrX\t166432950\t166432951\r\n-chrX\t84483714\t84483715\r\n-chrX\t98516735\t98516736\r\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/ExpressionData.txt --- a/test-data/ExpressionData.txt Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,957 +0,0 @@\n-#RefSeq_Gene Symbol\tchr1\tstart\tstop\tstrand\tdiff_exp\r\n-AF064749_Col6a3\tchr1\t92566771\t92800755\t-\t1\r\n-AK015559_4930472D16Rik\tchr1\t25020851\t25021989\t-\t1\r\n-AK030377_A330023F24Rik\tchr1\t196781953\t196826186\t-\t1\r\n-AK080193_A530079E22Rik\tchr1\t89401837\t89403491\t-\t1\r\n-AK082264_C230030N03Rik\tchr1\t34735043\t34781084\t+\t1\r\n-BC006931_AI597479\tchr1\t43153807\t43172843\t+\t1\r\n-BC021773_Glb1l\tchr1\t75193364\t75207353\t-\t1\r\n-BC023951_D1Ertd622e\tchr1\t99540054\t99558631\t-\t1\r\n-BC028767_3110009E18Rik\tchr1\t122017764\t122114603\t+\t1\r\n-BC031781_BC031781\tchr1\t182781250\t182798240\t+\t1\r\n-BC034187_BC035947\tchr1\t78493611\t78497758\t-\t1\r\n-BC043098_Fam168b\tchr1\t34870072\t34917183\t-\t1\r\n-BC049091_D1Bwg0212e\tchr1\t39592545\t39603734\t+\t1\r\n-BC049713_Ankrd45\tchr1\t163072817\t163099826\t+\t1\r\n-BC050813_4921511C04Rik\tchr1\t37157481\t37244861\t+\t1\r\n-BC051128_4921521F21Rik\tchr1\t65059273\t65079312\t-\t1\r\n-BC052693_2810422O20Rik\tchr1\t165924541\t165927371\t+\t1\r\n-BC052931_A630001G21Rik\tchr1\t87601462\t87674840\t-\t1\r\n-BC053100_5730559C18Rik\tchr1\t138110108\t138130841\t-\t1\r\n-BC054802_9630058J23Rik\tchr1\t181476521\t181558044\t+\t1\r\n-BC055845_2810025M15Rik\tchr1\t159342483\t159350353\t+\t1\r\n-BC055955_A130010J15Rik\tchr1\t194999663\t195004015\t+\t1\r\n-BC057872_Rab3gap2\tchr1\t187028006\t187110623\t+\t1\r\n-BC058417_2610017I09Rik\tchr1\t42648822\t42751667\t-\t1\r\n-BC059254_Phlpp\tchr1\t108042052\t108306367\t+\t1\r\n-BC070435_Fam123c\tchr1\t34620070\t34671545\t+\t1\r\n-BC070446_Fam135a\tchr1\t24017617\t24107170\t-\t1\r\n-BC071241_9430016H08Rik\tchr1\t57463192\t57497936\t+\t1\r\n-BC072639_2010300C02Rik\tchr1\t37646877\t37776659\t-\t1\r\n-BC080290_5033414K04Rik\tchr1\t84032539\t84360735\t-\t0\r\n-BC082310_9430031J16Rik\tchr1\t81073525\t81338329\t+\t0\r\n-BC089525_2310007B03Rik\tchr1\t95047933\t95063386\t-\t0\r\n-BC089561_Cep350\tchr1\t157692096\t157820375\t-\t0\r\n-BC147491_A230074B11Rik\tchr1\t37083441\t37133840\t+\t0\r\n-BC147657_9630028B13Rik\tchr1\t187253234\t187265698\t-\t0\r\n-ENSMUST00000027997_Rgs5\tchr1\t171625108\t171625913\t+\t0\r\n-ENSMUST00000051203_1700001G17Rik\tchr1\t33726669\t33727551\t+\t0\r\n-ENSMUST00000054333_A130050O07Rik\tchr1\t139823828\t139826840\t+\t0\r\n-ENSMUST00000056879_C230029F24Rik\tchr1\t49301475\t49397265\t+\t0\r\n-ENSMUST00000057543_A730013G03Rik\tchr1\t194659323\t194661397\t-\t0\r\n-ENSMUST00000062637_4930470H14Rik\tchr1\t175156866\t175201240\t+\t0\r\n-ENSMUST00000070048_ENSMUSG00000056128\tchr1\t92571736\t92576368\t+\t0\r\n-ENSMUST00000070987_EG433384\tchr1\t183781705\t183783320\t-\t0\r\n-ENSMUST00000072395_Olfr1406\tchr1\t175113651\t175120746\t-\t0\r\n-ENSMUST00000094288_Wdr64\tchr1\t177654798\t177798070\t+\t0\r\n-ENSMUST00000094950_Pgap1\tchr1\t54529849\t54614539\t-\t0\r\n-ENSMUST00000097776_Cnnm3\tchr1\t36567938\t36585164\t+\t0\r\n-EU429481_Igfn1\tchr1\t137825893\t137890307\t-\t0\r\n-FJ024495_Ildr2\tchr1\t168236882\t168239692\t-\t0\r\n-FJ210934_Unc80\tchr1\t66514856\t66556109\t+\t0\r\n-NM_001001565_Chpf\tchr1\t75470923\t75476437\t-\t0\r\n-NM_001001809_Olfr218\tchr1\t175130421\t175134469\t+\t0\r\n-NM_001001883_Hecw2\tchr1\t53867026\t54252002\t-\t0\r\n-NM_001003917_Atg9a\tchr1\t75177439\t75189181\t-\t0\r\n-NM_001004173_Sgpp2\tchr1\t78306692\t78416864\t+\t0\r\n-NM_001005423_Mreg\tchr1\t72170192\t72258895\t-\t0\r\n-NM_001005507_Smg7\tchr1\t154684125\t154750410\t-\t0\r\n-NM_001005508_Arhgap30\tchr1\t173319072\t173340822\t+\t0\r\n-NM_001005520_Olfr244\tchr1\t176032571\t176067605\t-\t0\r\n-NM_001008419_Aox3l1\tchr1\t58335180\t58437083\t+\t0\r\n-NM_001008426_EG433365\tchr1\t155721475\t155724001\t+\t0\r\n-NM_001008533_Adora1\tchr1\t136095799\t136181661\t-\t0\r\n-NM_001009940_Il19\tchr1\t132786042\t132915234\t-\t0\r\n-NM_001011525_Olfr1415\tchr1\t94376258\t94381054\t-\t0\r\n-NM_001011525_Olfr1415\tchr1\t94407669\t94418761\t-\t0\r\n-NM_001011684_Nms\tchr1\t38995917\t39007113\t+\t0\r\n-NM_001011873_Xkr9\tchr1\t13658862\t13691794\t+\t0\r\n-NM_001011874_Xkr4\tchr1\t3203722\t3713108\t-\t0\r\n-NM_001012330_Zfp238\tchr1\t179359958\t179380892\t+\t0\r\n-NM_001013374_Lman2l\tchr1\t36362897\t36502078\t-\t0\r\n-NM_001013382_Lrrc52\tchr1\t169375806\t169397136\t-\t0\r\n-NM_001013771_Gm973\tchr1\t59573136\t59693241\t+\t0\r\n-NM_001013779_Aim2\tchr1\t175385835\t175396165\t+\t0\r\n-NM_001014974_Ttll4\tchr1\t74708314\t74748400\t+\t0\r\n-NM_001024721_BC094916\tchr1\t175451304\t175466101\t-\t0\r\n-NM_001024945_Qsox1\tchr1\t157625296\t157670499\t-\t0\r\n-NM_001025156_Ccdc93'..b's\tchr1\t130260284\t130314013\t-\t0\r\n-NM_177587_Aqp12\tchr1\t94886487\t94908846\t+\t0\r\n-NM_177604_AA986860\tchr1\t132628563\t132644539\t+\t0\r\n-NM_177643_Zfp281\tchr1\t138487073\t138526617\t+\t0\r\n-NM_177646_Dgkd\tchr1\t89749836\t89841946\t+\t0\r\n-NM_177722_6030422M02Rik\tchr1\t9898713\t9932156\t+\t0\r\n-NM_177723_Vsig8\tchr1\t174486069\t174513273\t+\t0\r\n-NM_177724_D230039L06Rik\tchr1\t180426979\t180686112\t+\t0\r\n-NM_177756_Glt25d2\tchr1\t154223175\t154357825\t+\t0\r\n-NM_177757_Kif26b\tchr1\t180720593\t180862983\t+\t0\r\n-NM_177781_Trpa1\tchr1\t14861962\t14909072\t-\t0\r\n-NM_177834_Cpa6\tchr1\t10314801\t10710026\t-\t0\r\n-NM_177838_Fam163a\tchr1\t157923096\t158135544\t-\t0\r\n-NM_177839_Tnn\tchr1\t161966935\t162084477\t-\t0\r\n-NM_178051_Mterfd2\tchr1\t95195779\t95202630\t-\t0\r\n-NM_178055_Dnajb2\tchr1\t75233016\t75242264\t+\t0\r\n-NM_178119_Agap1\tchr1\t91351421\t91791845\t+\t0\r\n-NM_178241_Il8ra\tchr1\t74238380\t74241205\t-\t0\r\n-NM_178243_5830403L16Rik\tchr1\t155697272\t155747352\t-\t0\r\n-NM_178244_Teddm1\tchr1\t155724147\t155740188\t+\t0\r\n-NM_178399_3110035E14Rik\tchr1\t9591248\t9617222\t+\t0\r\n-NM_178405_Atp1a2\tchr1\t174201852\t174233438\t-\t0\r\n-NM_178593_Rcsd1\tchr1\t167572007\t167639868\t-\t0\r\n-NM_178598_Tagln2\tchr1\t174430123\t174475991\t+\t0\r\n-NM_178601_Imp4\tchr1\t34496377\t34511555\t+\t0\r\n-NM_178632_Ints7\tchr1\t193399085\t193447550\t+\t0\r\n-NM_178653_Sccpdh\tchr1\t181598088\t181617593\t+\t0\r\n-NM_178690_Rab3gap1\tchr1\t129765355\t129840723\t+\t0\r\n-NM_178691_Yod1\tchr1\t132612680\t132618643\t+\t0\r\n-NM_178692_C130074G19Rik\tchr1\t186695805\t186707077\t-\t0\r\n-NM_178775_Rps6kc1\tchr1\t192524091\t192736016\t-\t0\r\n-NM_178779_Rnf152\tchr1\t107176426\t107253513\t-\t0\r\n-NM_178874_Tmcc2\tchr1\t134252895\t134288369\t-\t0\r\n-NM_178883_Gorab\tchr1\t165315039\t165340946\t-\t0\r\n-NM_178884_Obsl1\tchr1\t75482401\t75503218\t-\t0\r\n-NM_181405_Rnpepl1\tchr1\t94807467\t94817954\t+\t0\r\n-NM_181546_Syt14\tchr1\t194713536\t194861959\t-\t0\r\n-NM_181750_R3hdm1\tchr1\t129999892\t130134312\t+\t0\r\n-NM_181796_Gstp2\tchr1\t193897651\t193905509\t-\t0\r\n-NM_182716_Nfasc\tchr1\t134445291\t134638354\t-\t0\r\n-NM_182930_Plekha6\tchr1\t135077806\t135200008\t+\t0\r\n-NM_183019_Arhgef4\tchr1\t34788954\t34873560\t+\t0\r\n-NM_183022_Accn4\tchr1\t75447063\t75470207\t+\t0\r\n-NM_183027_Ap1s3\tchr1\t79591820\t79668545\t-\t0\r\n-NM_183028_Pcmtd1\tchr1\t7079053\t7163709\t+\t0\r\n-NM_183124_Defb41\tchr1\t18241071\t18350659\t-\t0\r\n-NM_183355_Pbx1\tchr1\t170049495\t170512777\t-\t0\r\n-NM_183391_Tnfsf18\tchr1\t163373523\t163524094\t+\t0\r\n-NM_194333_Slc23a3\tchr1\t75120731\t75130464\t-\t0\r\n-NM_198006_6330578E17Rik\tchr1\t37473934\t37474944\t-\t0\r\n-NM_198006_6330578E17Rik\tchr1\t37477057\t37486928\t-\t0\r\n-NM_198028_Serpinb10\tchr1\t109425580\t109445838\t+\t0\r\n-NM_198127_Abi2\tchr1\t60466022\t60537998\t+\t0\r\n-NM_198247_Sertad4\tchr1\t194670313\t194693726\t-\t0\r\n-NM_198303_Eif5b\tchr1\t38054627\t38112414\t+\t0\r\n-NM_198652_6430706D22Rik\tchr1\t90158880\t90174174\t-\t0\r\n-NM_198653_Iars2\tchr1\t187109458\t187153280\t-\t0\r\n-NM_198654_Nsl1\tchr1\t192886918\t192919389\t+\t0\r\n-NM_198680_Serpinb3b\tchr1\t109033488\t109059720\t-\t0\r\n-NM_198899_Ugcgl1\tchr1\t36196873\t36301555\t-\t0\r\n-NM_198934_Pou2f1\tchr1\t167804181\t167932753\t-\t0\r\n-NM_199007_Sgol2\tchr1\t58026657\t58085164\t+\t0\r\n-NM_199021_Dpp10\tchr1\t125044486\t126749525\t-\t0\r\n-NM_201363_Serpinb3c\tchr1\t109088051\t109198931\t-\t0\r\n-NM_201376_Serpinb3d\tchr1\t108974770\t108980057\t-\t0\r\n-NM_201641_Ugt1a10\tchr1\t89922380\t90115570\t+\t0\r\n-NM_206896_Olfr12\tchr1\t94516341\t94538591\t+\t0\r\n-NM_207031_Ano7\tchr1\t95270385\t95302271\t+\t0\r\n-NM_207137_Olfr417\tchr1\t176299050\t176299979\t+\t0\r\n-NM_207137_Olfr417\tchr1\t176321202\t176322113\t+\t0\r\n-NM_207158_Olfr427\tchr1\t176028781\t176030538\t+\t0\r\n-NM_207225_Hdac4\tchr1\t93755950\t94103099\t-\t0\r\n-NM_207228_Tsga10\tchr1\t37783457\t37922148\t-\t0\r\n-NM_207233_C1ql2\tchr1\t122196386\t122239751\t+\t0\r\n-NM_207281_4832428D23Rik\tchr1\t44260915\t44515719\t-\t0\r\n-NM_207583_Fam5b\tchr1\t160175402\t160286644\t-\t0\r\n-NM_207653_Cflar\tchr1\t58768296\t58813658\t+\t0\r\n-NM_207653_Cflar\tchr1\t58813703\t58815725\t+\t0\r\n-NM_213616_Atp2b4\tchr1\t135602265\t135697538\t-\t0\r\n-NR_002840_Gas5\tchr1\t162964758\t162968663\t+\t0\r\n-NR_002858_EG241041\tchr1\t21268965\t21306401\t-\t0\r\n-NR_002870_Dnm3os\tchr1\t164119785\t164155671\t+\t0\r\n-NR_003623_EG277333\tchr1\t182251970\t182262902\t-\t0\r\n-NR_026896_4931440L10Rik\tchr1\t136437533\t136449760\t-\t0\r\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/features.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features.txt Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,957 @@\n+#RefSeq_Gene Symbol\tchr1\tstart\tstop\tstrand\tdiff_exp\r\n+AF064749_Col6a3\tchr1\t92566771\t92800755\t-\t1\r\n+AK015559_4930472D16Rik\tchr1\t25020851\t25021989\t-\t1\r\n+AK030377_A330023F24Rik\tchr1\t196781953\t196826186\t-\t1\r\n+AK080193_A530079E22Rik\tchr1\t89401837\t89403491\t-\t1\r\n+AK082264_C230030N03Rik\tchr1\t34735043\t34781084\t+\t1\r\n+BC006931_AI597479\tchr1\t43153807\t43172843\t+\t1\r\n+BC021773_Glb1l\tchr1\t75193364\t75207353\t-\t1\r\n+BC023951_D1Ertd622e\tchr1\t99540054\t99558631\t-\t1\r\n+BC028767_3110009E18Rik\tchr1\t122017764\t122114603\t+\t1\r\n+BC031781_BC031781\tchr1\t182781250\t182798240\t+\t1\r\n+BC034187_BC035947\tchr1\t78493611\t78497758\t-\t1\r\n+BC043098_Fam168b\tchr1\t34870072\t34917183\t-\t1\r\n+BC049091_D1Bwg0212e\tchr1\t39592545\t39603734\t+\t1\r\n+BC049713_Ankrd45\tchr1\t163072817\t163099826\t+\t1\r\n+BC050813_4921511C04Rik\tchr1\t37157481\t37244861\t+\t1\r\n+BC051128_4921521F21Rik\tchr1\t65059273\t65079312\t-\t1\r\n+BC052693_2810422O20Rik\tchr1\t165924541\t165927371\t+\t1\r\n+BC052931_A630001G21Rik\tchr1\t87601462\t87674840\t-\t1\r\n+BC053100_5730559C18Rik\tchr1\t138110108\t138130841\t-\t1\r\n+BC054802_9630058J23Rik\tchr1\t181476521\t181558044\t+\t1\r\n+BC055845_2810025M15Rik\tchr1\t159342483\t159350353\t+\t1\r\n+BC055955_A130010J15Rik\tchr1\t194999663\t195004015\t+\t1\r\n+BC057872_Rab3gap2\tchr1\t187028006\t187110623\t+\t1\r\n+BC058417_2610017I09Rik\tchr1\t42648822\t42751667\t-\t1\r\n+BC059254_Phlpp\tchr1\t108042052\t108306367\t+\t1\r\n+BC070435_Fam123c\tchr1\t34620070\t34671545\t+\t1\r\n+BC070446_Fam135a\tchr1\t24017617\t24107170\t-\t1\r\n+BC071241_9430016H08Rik\tchr1\t57463192\t57497936\t+\t1\r\n+BC072639_2010300C02Rik\tchr1\t37646877\t37776659\t-\t1\r\n+BC080290_5033414K04Rik\tchr1\t84032539\t84360735\t-\t0\r\n+BC082310_9430031J16Rik\tchr1\t81073525\t81338329\t+\t0\r\n+BC089525_2310007B03Rik\tchr1\t95047933\t95063386\t-\t0\r\n+BC089561_Cep350\tchr1\t157692096\t157820375\t-\t0\r\n+BC147491_A230074B11Rik\tchr1\t37083441\t37133840\t+\t0\r\n+BC147657_9630028B13Rik\tchr1\t187253234\t187265698\t-\t0\r\n+ENSMUST00000027997_Rgs5\tchr1\t171625108\t171625913\t+\t0\r\n+ENSMUST00000051203_1700001G17Rik\tchr1\t33726669\t33727551\t+\t0\r\n+ENSMUST00000054333_A130050O07Rik\tchr1\t139823828\t139826840\t+\t0\r\n+ENSMUST00000056879_C230029F24Rik\tchr1\t49301475\t49397265\t+\t0\r\n+ENSMUST00000057543_A730013G03Rik\tchr1\t194659323\t194661397\t-\t0\r\n+ENSMUST00000062637_4930470H14Rik\tchr1\t175156866\t175201240\t+\t0\r\n+ENSMUST00000070048_ENSMUSG00000056128\tchr1\t92571736\t92576368\t+\t0\r\n+ENSMUST00000070987_EG433384\tchr1\t183781705\t183783320\t-\t0\r\n+ENSMUST00000072395_Olfr1406\tchr1\t175113651\t175120746\t-\t0\r\n+ENSMUST00000094288_Wdr64\tchr1\t177654798\t177798070\t+\t0\r\n+ENSMUST00000094950_Pgap1\tchr1\t54529849\t54614539\t-\t0\r\n+ENSMUST00000097776_Cnnm3\tchr1\t36567938\t36585164\t+\t0\r\n+EU429481_Igfn1\tchr1\t137825893\t137890307\t-\t0\r\n+FJ024495_Ildr2\tchr1\t168236882\t168239692\t-\t0\r\n+FJ210934_Unc80\tchr1\t66514856\t66556109\t+\t0\r\n+NM_001001565_Chpf\tchr1\t75470923\t75476437\t-\t0\r\n+NM_001001809_Olfr218\tchr1\t175130421\t175134469\t+\t0\r\n+NM_001001883_Hecw2\tchr1\t53867026\t54252002\t-\t0\r\n+NM_001003917_Atg9a\tchr1\t75177439\t75189181\t-\t0\r\n+NM_001004173_Sgpp2\tchr1\t78306692\t78416864\t+\t0\r\n+NM_001005423_Mreg\tchr1\t72170192\t72258895\t-\t0\r\n+NM_001005507_Smg7\tchr1\t154684125\t154750410\t-\t0\r\n+NM_001005508_Arhgap30\tchr1\t173319072\t173340822\t+\t0\r\n+NM_001005520_Olfr244\tchr1\t176032571\t176067605\t-\t0\r\n+NM_001008419_Aox3l1\tchr1\t58335180\t58437083\t+\t0\r\n+NM_001008426_EG433365\tchr1\t155721475\t155724001\t+\t0\r\n+NM_001008533_Adora1\tchr1\t136095799\t136181661\t-\t0\r\n+NM_001009940_Il19\tchr1\t132786042\t132915234\t-\t0\r\n+NM_001011525_Olfr1415\tchr1\t94376258\t94381054\t-\t0\r\n+NM_001011525_Olfr1415\tchr1\t94407669\t94418761\t-\t0\r\n+NM_001011684_Nms\tchr1\t38995917\t39007113\t+\t0\r\n+NM_001011873_Xkr9\tchr1\t13658862\t13691794\t+\t0\r\n+NM_001011874_Xkr4\tchr1\t3203722\t3713108\t-\t0\r\n+NM_001012330_Zfp238\tchr1\t179359958\t179380892\t+\t0\r\n+NM_001013374_Lman2l\tchr1\t36362897\t36502078\t-\t0\r\n+NM_001013382_Lrrc52\tchr1\t169375806\t169397136\t-\t0\r\n+NM_001013771_Gm973\tchr1\t59573136\t59693241\t+\t0\r\n+NM_001013779_Aim2\tchr1\t175385835\t175396165\t+\t0\r\n+NM_001014974_Ttll4\tchr1\t74708314\t74748400\t+\t0\r\n+NM_001024721_BC094916\tchr1\t175451304\t175466101\t-\t0\r\n+NM_001024945_Qsox1\tchr1\t157625296\t157670499\t-\t0\r\n+NM_001025156_Ccdc93'..b's\tchr1\t130260284\t130314013\t-\t0\r\n+NM_177587_Aqp12\tchr1\t94886487\t94908846\t+\t0\r\n+NM_177604_AA986860\tchr1\t132628563\t132644539\t+\t0\r\n+NM_177643_Zfp281\tchr1\t138487073\t138526617\t+\t0\r\n+NM_177646_Dgkd\tchr1\t89749836\t89841946\t+\t0\r\n+NM_177722_6030422M02Rik\tchr1\t9898713\t9932156\t+\t0\r\n+NM_177723_Vsig8\tchr1\t174486069\t174513273\t+\t0\r\n+NM_177724_D230039L06Rik\tchr1\t180426979\t180686112\t+\t0\r\n+NM_177756_Glt25d2\tchr1\t154223175\t154357825\t+\t0\r\n+NM_177757_Kif26b\tchr1\t180720593\t180862983\t+\t0\r\n+NM_177781_Trpa1\tchr1\t14861962\t14909072\t-\t0\r\n+NM_177834_Cpa6\tchr1\t10314801\t10710026\t-\t0\r\n+NM_177838_Fam163a\tchr1\t157923096\t158135544\t-\t0\r\n+NM_177839_Tnn\tchr1\t161966935\t162084477\t-\t0\r\n+NM_178051_Mterfd2\tchr1\t95195779\t95202630\t-\t0\r\n+NM_178055_Dnajb2\tchr1\t75233016\t75242264\t+\t0\r\n+NM_178119_Agap1\tchr1\t91351421\t91791845\t+\t0\r\n+NM_178241_Il8ra\tchr1\t74238380\t74241205\t-\t0\r\n+NM_178243_5830403L16Rik\tchr1\t155697272\t155747352\t-\t0\r\n+NM_178244_Teddm1\tchr1\t155724147\t155740188\t+\t0\r\n+NM_178399_3110035E14Rik\tchr1\t9591248\t9617222\t+\t0\r\n+NM_178405_Atp1a2\tchr1\t174201852\t174233438\t-\t0\r\n+NM_178593_Rcsd1\tchr1\t167572007\t167639868\t-\t0\r\n+NM_178598_Tagln2\tchr1\t174430123\t174475991\t+\t0\r\n+NM_178601_Imp4\tchr1\t34496377\t34511555\t+\t0\r\n+NM_178632_Ints7\tchr1\t193399085\t193447550\t+\t0\r\n+NM_178653_Sccpdh\tchr1\t181598088\t181617593\t+\t0\r\n+NM_178690_Rab3gap1\tchr1\t129765355\t129840723\t+\t0\r\n+NM_178691_Yod1\tchr1\t132612680\t132618643\t+\t0\r\n+NM_178692_C130074G19Rik\tchr1\t186695805\t186707077\t-\t0\r\n+NM_178775_Rps6kc1\tchr1\t192524091\t192736016\t-\t0\r\n+NM_178779_Rnf152\tchr1\t107176426\t107253513\t-\t0\r\n+NM_178874_Tmcc2\tchr1\t134252895\t134288369\t-\t0\r\n+NM_178883_Gorab\tchr1\t165315039\t165340946\t-\t0\r\n+NM_178884_Obsl1\tchr1\t75482401\t75503218\t-\t0\r\n+NM_181405_Rnpepl1\tchr1\t94807467\t94817954\t+\t0\r\n+NM_181546_Syt14\tchr1\t194713536\t194861959\t-\t0\r\n+NM_181750_R3hdm1\tchr1\t129999892\t130134312\t+\t0\r\n+NM_181796_Gstp2\tchr1\t193897651\t193905509\t-\t0\r\n+NM_182716_Nfasc\tchr1\t134445291\t134638354\t-\t0\r\n+NM_182930_Plekha6\tchr1\t135077806\t135200008\t+\t0\r\n+NM_183019_Arhgef4\tchr1\t34788954\t34873560\t+\t0\r\n+NM_183022_Accn4\tchr1\t75447063\t75470207\t+\t0\r\n+NM_183027_Ap1s3\tchr1\t79591820\t79668545\t-\t0\r\n+NM_183028_Pcmtd1\tchr1\t7079053\t7163709\t+\t0\r\n+NM_183124_Defb41\tchr1\t18241071\t18350659\t-\t0\r\n+NM_183355_Pbx1\tchr1\t170049495\t170512777\t-\t0\r\n+NM_183391_Tnfsf18\tchr1\t163373523\t163524094\t+\t0\r\n+NM_194333_Slc23a3\tchr1\t75120731\t75130464\t-\t0\r\n+NM_198006_6330578E17Rik\tchr1\t37473934\t37474944\t-\t0\r\n+NM_198006_6330578E17Rik\tchr1\t37477057\t37486928\t-\t0\r\n+NM_198028_Serpinb10\tchr1\t109425580\t109445838\t+\t0\r\n+NM_198127_Abi2\tchr1\t60466022\t60537998\t+\t0\r\n+NM_198247_Sertad4\tchr1\t194670313\t194693726\t-\t0\r\n+NM_198303_Eif5b\tchr1\t38054627\t38112414\t+\t0\r\n+NM_198652_6430706D22Rik\tchr1\t90158880\t90174174\t-\t0\r\n+NM_198653_Iars2\tchr1\t187109458\t187153280\t-\t0\r\n+NM_198654_Nsl1\tchr1\t192886918\t192919389\t+\t0\r\n+NM_198680_Serpinb3b\tchr1\t109033488\t109059720\t-\t0\r\n+NM_198899_Ugcgl1\tchr1\t36196873\t36301555\t-\t0\r\n+NM_198934_Pou2f1\tchr1\t167804181\t167932753\t-\t0\r\n+NM_199007_Sgol2\tchr1\t58026657\t58085164\t+\t0\r\n+NM_199021_Dpp10\tchr1\t125044486\t126749525\t-\t0\r\n+NM_201363_Serpinb3c\tchr1\t109088051\t109198931\t-\t0\r\n+NM_201376_Serpinb3d\tchr1\t108974770\t108980057\t-\t0\r\n+NM_201641_Ugt1a10\tchr1\t89922380\t90115570\t+\t0\r\n+NM_206896_Olfr12\tchr1\t94516341\t94538591\t+\t0\r\n+NM_207031_Ano7\tchr1\t95270385\t95302271\t+\t0\r\n+NM_207137_Olfr417\tchr1\t176299050\t176299979\t+\t0\r\n+NM_207137_Olfr417\tchr1\t176321202\t176322113\t+\t0\r\n+NM_207158_Olfr427\tchr1\t176028781\t176030538\t+\t0\r\n+NM_207225_Hdac4\tchr1\t93755950\t94103099\t-\t0\r\n+NM_207228_Tsga10\tchr1\t37783457\t37922148\t-\t0\r\n+NM_207233_C1ql2\tchr1\t122196386\t122239751\t+\t0\r\n+NM_207281_4832428D23Rik\tchr1\t44260915\t44515719\t-\t0\r\n+NM_207583_Fam5b\tchr1\t160175402\t160286644\t-\t0\r\n+NM_207653_Cflar\tchr1\t58768296\t58813658\t+\t0\r\n+NM_207653_Cflar\tchr1\t58813703\t58815725\t+\t0\r\n+NM_213616_Atp2b4\tchr1\t135602265\t135697538\t-\t0\r\n+NR_002840_Gas5\tchr1\t162964758\t162968663\t+\t0\r\n+NR_002858_EG241041\tchr1\t21268965\t21306401\t-\t0\r\n+NR_002870_Dnm3os\tchr1\t164119785\t164155671\t+\t0\r\n+NR_003623_EG277333\tchr1\t182251970\t182262902\t-\t0\r\n+NR_026896_4931440L10Rik\tchr1\t136437533\t136449760\t-\t0\r\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/features_per_peak1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_per_peak1.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,70 @@\n+#peak.chr\tpeak.start\tpeak.end\tgene.id_1\tstrand_1\tTSS_1\tTES_1\tdist_closest_1\tdist_TSS_1\tdist_TES_1\tdirection_1\toverlap_gene_1\toverlap_promoter_1\tgene.id_2\tstrand_2\tTSS_2\tTES_2\tdist_closest_2\tdist_TSS_2\tdist_TES_2\tdirection_2\toverlap_gene_2\toverlap_promoter_2\tgene.id_3\tstrand_3\tTSS_3\tTES_3\tdist_closest_3\tdist_TSS_3\tdist_TES_3\tdirection_3\toverlap_gene_3\toverlap_promoter_3\tgene.id_4\tstrand_4\tTSS_4\tTES_4\tdist_closest_4\tdist_TSS_4\tdist_TES_4\tdirection_4\toverlap_gene_4\toverlap_promoter_4\n+chr1\t10617233\t10617437\tNM_177834_Cpa6\t-\t10710026\t10314801\t0\t92589\t302432\t.\t1\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t108747519\t108747791\tNM_009190_Vps4b\t-\t108739123\t108665873\t8396\t8396\t81646\tU\t0\t1\tNM_009257_Serpinb5\t+\t108757652\t108779925\t9861\t9861\t32134\tU\t0\t1\tNM_027971_Serpinb12\t+\t108831026\t108853655\t83235\t83235\t105864\tU\t0\t0\tNM_027534_Kdsr\t-\t108656357\t108617007\t91162\t91162\t130512\tU\t0\t0\n+chr1\t120760212\t120760461\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t132950929\t132951247\tNM_010548_Il10\t+\t132916424\t132921547\t29382\t34505\t29382\tD\t0\t0\tNM_001009940_Il19\t-\t132915234\t132786042\t35695\t35695\t164887\tU\t0\t0\tNM_008551_Mapkapk2\t-\t133013820\t132950274\t0\t62573\t655\t.\t1\t0\tNM_145508_Dyrk3\t-\t133034897\t133018921\t67674\t83650\t67674\tD\t0\t0\n+chr1\t133114860\t133115015\tNM_018750_Rassf5\t-\t133144761\t133072991\t0\t29746\t41869\t.\t1\t0\tNM_019777_Ikbke\t-\t133176163\t133151052\t36037\t61148\t36037\tD\t0\t0\tNM_001136070_Lgtn\t+\t133049773\t133084235\t30625\t65087\t30625\tD\t0\t0\tNM_145508_Dyrk3\t-\t133034897\t133018921\t79963\t79963\t95939\tU\t0\t0\n+chr1\t135582677\t135582828\tNM_001159649_Lax1\t-\t135586665\t135575626\t0\t3837\t7051\t.\t1\t0\tNM_144530_Zc3h11a\t-\t135557956\t135516445\t24721\t24721\t66232\tU\t0\t0\tNM_213616_Atp2b4\t-\t135697538\t135602265\t19437\t114710\t19437\tD\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t135851853\t135852218\tNM_054077_Prelp\t-\t135865173\t135806855\t0\t12955\t44998\t.\t1\t0\tNM_054076_Optc\t-\t135805299\t135787973\t46554\t46554\t63880\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t136956468\t136956598\tNM_007955_Ptprv\t-\t137029151\t137004306\t47708\t72553\t47708\tD\t0\t0\tNM_026823_Arl8a\t+\t137043216\t137053347\t86618\t86618\t96749\tU\t0\t0\tNM_026024_Ube2t\t+\t136857731\t136870739\t85729\t98737\t85729\tD\t0\t0\tNM_134438_Gpr37l1\t-\t137069087\t137054243\t97645\t112489\t97645\tD\t0\t0\n+chr1\t13829227\t13829564\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t138437726\t138437860\tNM_177643_Zfp281\t+\t138487073\t138526617\t49213\t49213\t88757\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t140381656\t140381785\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t145591041\t145591176\tNM_001038592_Glrx2\t+\t145585774\t145608282\t0\t5267\t17106\t.\t1\t0\tNM_019562_Uchl5\t+\t145623774\t145654586\t32598\t32598\t63410\tU\t0\t0\tNM_013835_Trove2\t-\t145624178\t145597816\t6640\t33002\t6640\tD\t0\t0\tNM_145991_Cdc73\t-\t145549936\t145274292\t41105\t41105\t316749\tU\t0\t0\n+chr1\t154971572\t154971673\tNM_008485_Lamc2\t-\t155033557\t154969890\t0\t61884\t1682\t.\t1\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t155123313\t155123435\tNM_010683_Lamc1\t-\t155179906\t155065803\t0\t56471\t57510\t.\t1\t0\tNM_008485_Lamc2\t-\t155033557\t154969890\t89756\t89756\t153423\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158510523\t158510813\tNM_009230_Soat1\t-\t158417632\t158354679\t92891\t92891\t155844\tU\t0\t0\tNM_023141_Tor3a\t-\t158604477\t158583760\t72947\t93664\t72947\tD\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158537267\t158537411\tNM_023141_Tor3a\t-\t158604477\t158583760\t46349\t67066\t46349\tD\t0\t0\tNM_145413_Fam20b\t-\t158649180\t158608676\t71265\t111769\t71265\tD\t0\t0\tNM_009230_Soat1\t-\t158417632\t158354679\t119635\t119635\t182588\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158580638\t158580759\tNM_023141_Tor3a\t-\t158604477\t158583760\t3001\t23718\t3001\tD\t0\t0\tNM_145413_Fam20b\t-\t158649180\t158608676\t27917\t68421\t27917\tD\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158835251\t158835391\tNM_028333_Angptl1\t+\t158769061\t158791209\t44042\t66190\t44042\tD\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+ch'..b'1\t60929\tU\t0\t1\tNM_023645_Kdelc1\t-\t44177102\t44143458\t18347\t18347\t51991\tU\t0\t0\tNM_144558_Bivm\t+\t44175822\t44201615\t0\t19627\t5976\t.\t1\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t52625416\t52625560\tNM_008667_Nab1\t-\t52611216\t52487127\t14200\t14200\t138289\tU\t0\t0\tNM_001142647_Tmem194b\t+\t52687569\t52708760\t62009\t62009\t83200\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t54631692\t54631815\tENSMUST00000094950_Pgap1\t-\t54614539\t54529849\t17153\t17153\t101843\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t55283572\t55283675\tNM_028713_Rftn2\t-\t55283748\t55227030\t0\t73\t56542\t.\t1\t1\tNM_175439_Mars2\t+\t55294084\t55297625\t10409\t10409\t13950\tU\t0\t0\tNM_025283_Mobkl3\t+\t55187734\t55211736\t71836\t95838\t71836\tD\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t63664888\t63665018\tNM_011780_Adam23\t+\t63640970\t63642850\t22038\t23918\t22038\tD\t0\t0\tNM_029696_Mdh1b\t-\t63776894\t63745401\t80383\t111876\t80383\tD\t0\t0\tNM_172422_Fastkd2\t+\t63777134\t63803028\t112116\t112116\t138010\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t72769824\t72770056\tNM_176980_Ankar\t-\t72747143\t72689581\t22681\t22681\t80243\tU\t0\t0\tNM_008342_Igfbp2\t+\t72840313\t72899038\t70257\t70257\t128982\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t72770058\t72770226\tNM_176980_Ankar\t-\t72747143\t72689581\t22915\t22915\t80477\tU\t0\t0\tNM_008342_Igfbp2\t+\t72840313\t72899038\t70087\t70087\t128812\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t72815517\t72815742\tNM_008342_Igfbp2\t+\t72840313\t72899038\t24571\t24571\t83296\tU\t0\t0\tNM_176980_Ankar\t-\t72747143\t72689581\t68374\t68374\t125936\tU\t0\t0\tNM_010518_Igfbp5\t-\t72921468\t72904507\t88765\t105726\t88765\tD\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t75481920\t75482054\tNM_001001565_Chpf\t-\t75476437\t75470923\t5483\t5483\t10997\tU\t0\t1\tNM_178884_Obsl1\t-\t75503218\t75482401\t347\t21164\t347\tD\t0\t0\tNM_010564_Inha\t+\t75503647\t75506924\t21593\t21593\t24870\tU\t0\t0\tNM_183022_Accn4\t+\t75447063\t75470207\t11713\t34857\t11713\tD\t0\t0\n+chr1\t77457642\t77457791\tNM_007936_Epha4\t-\t77511653\t77280640\t0\t53862\t177002\t.\t1\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t78630893\t78631160\tNM_028817_Acsl3\t+\t78654388\t78743434\t23228\t23228\t112274\tU\t0\t0\tNM_011811_Farsb\t-\t78506689\t78414533\t124204\t124204\t216360\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t88408969\t88409267\tNM_172974_Cops7b\t+\t88478926\t88503950\t69659\t69659\t94683\tU\t0\t0\tNM_008801_Pde6d\t-\t88479102\t88427331\t18064\t69835\t18064\tD\t0\t0\tNM_010341_Nmur1\t-\t88297441\t88282479\t111528\t111528\t126490\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t89989553\t89989714\tNM_201641_Ugt1a10\t+\t89922380\t90115570\t0\t67173\t125856\t.\t1\t0\tNM_008299_Dnajb3\t-\t90102337\t90101307\t111593\t112623\t111593\tD\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t90412932\t90413132\tNM_008132_Glrp1\t-\t90406631\t90396446\t6301\t6301\t16486\tU\t0\t1\tNM_029269_Spp2\t+\t90303568\t90373213\t39719\t109364\t39719\tD\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t90592499\t90592629\tNM_177305_Arl4c\t-\t90617572\t90569702\t0\t24943\t22797\t.\t1\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t91496003\t91496145\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t91496155\t91496319\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t92070253\t92070431\tNM_007722_Cxcr7\t+\t92100063\t92112863\t29632\t29632\t42432\tU\t0\t0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t95186508\t95186637\tNM_178051_Mterfd2\t-\t95202630\t95195779\t9142\t15993\t9142\tD\t0\t0\tNM_023200_Ppp1r7\t+\t95239431\t95266345\t52794\t52794\t79708\tU\t0\t0\tNM_080850_Pask\t-\t95240039\t95205357\t18720\t53402\t18720\tD\t0\t0\tNM_172463_Sned1\t+\t95132418\t95197642\t0\t54090\t11005\t.\t1\t0\n+chr1\t9619046\t9619167\tNM_178399_3110035E14Rik\t+\t9591248\t9617222\t1824\t27798\t1824\tD\t0\t0\tNM_008651_Mybl1\t-\t9690280\t9635825\t16658\t71113\t16658\tD\t0\t0\tNM_175236_Adhfe1\t+\t9538049\t9570746\t48300\t80997\t48300\tD\t0\t0\tNM_021511_Rrs1\t+\t9535513\t9537532\t81514\t83533\t81514\tD\t0\t0\n+chr1\t9619175\t9619382\tNM_178399_3110035E14Rik\t+\t9591248\t9617222\t1953\t27927\t1953\tD\t0\t0\tNM_008651_Mybl1\t-\t9690280\t9635825\t16443\t70898\t16443\tD\t0\t0\tNM_175236_Adhfe1\t+\t9538049\t9570746\t48429\t81126\t48429\tD\t0\t0\tNM_021511_Rrs1\t+\t9535513\t9537532\t81643\t83662\t81643\tD\t0\t0\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/features_per_peak2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_per_peak2.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,140 @@\n+#peak.chr\tpeak.start\tpeak.end\tgene.id\tstrand\tTSS\tTES\tdist_closest\tdist_TSS\tdist_TES\tdirection\toverlap_gene\toverlap_promoter\n+chr1\t10617233\t10617437\tNM_177834_Cpa6\t-\t10710026\t10314801\t0\t92589\t302432\t.\t1\t0\n+chr1\t108747519\t108747791\tNM_009190_Vps4b\t-\t108739123\t108665873\t8396\t8396\t81646\tU\t0\t0\n+chr1\t108747519\t108747791\tNM_009257_Serpinb5\t+\t108757652\t108779925\t9861\t9861\t32134\tU\t0\t0\n+chr1\t108747519\t108747791\tNM_027971_Serpinb12\t+\t108831026\t108853655\t83235\t83235\t105864\tU\t0\t0\n+chr1\t108747519\t108747791\tNM_027534_Kdsr\t-\t108656357\t108617007\t91162\t91162\t130512\tU\t0\t0\n+chr1\t120760212\t120760461\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t132950929\t132951247\tNM_010548_Il10\t+\t132916424\t132921547\t29382\t34505\t29382\tD\t0\t0\n+chr1\t132950929\t132951247\tNM_001009940_Il19\t-\t132915234\t132786042\t35695\t35695\t164887\tU\t0\t0\n+chr1\t132950929\t132951247\tNM_008551_Mapkapk2\t-\t133013820\t132950274\t0\t62573\t655\t.\t1\t0\n+chr1\t132950929\t132951247\tNM_145508_Dyrk3\t-\t133034897\t133018921\t67674\t83650\t67674\tD\t0\t0\n+chr1\t133114860\t133115015\tNM_018750_Rassf5\t-\t133144761\t133072991\t0\t29746\t41869\t.\t1\t0\n+chr1\t133114860\t133115015\tNM_019777_Ikbke\t-\t133176163\t133151052\t36037\t61148\t36037\tD\t0\t0\n+chr1\t133114860\t133115015\tNM_001136070_Lgtn\t+\t133049773\t133084235\t30625\t65087\t30625\tD\t0\t0\n+chr1\t133114860\t133115015\tNM_145508_Dyrk3\t-\t133034897\t133018921\t79963\t79963\t95939\tU\t0\t0\n+chr1\t135582677\t135582828\tNM_001159649_Lax1\t-\t135586665\t135575626\t0\t3837\t7051\t.\t1\t0\n+chr1\t135582677\t135582828\tNM_144530_Zc3h11a\t-\t135557956\t135516445\t24721\t24721\t66232\tU\t0\t0\n+chr1\t135582677\t135582828\tNM_213616_Atp2b4\t-\t135697538\t135602265\t19437\t114710\t19437\tD\t0\t0\n+chr1\t135851853\t135852218\tNM_054077_Prelp\t-\t135865173\t135806855\t0\t12955\t44998\t.\t1\t0\n+chr1\t135851853\t135852218\tNM_054076_Optc\t-\t135805299\t135787973\t46554\t46554\t63880\tU\t0\t0\n+chr1\t136956468\t136956598\tNM_007955_Ptprv\t-\t137029151\t137004306\t47708\t72553\t47708\tD\t0\t0\n+chr1\t136956468\t136956598\tNM_026823_Arl8a\t+\t137043216\t137053347\t86618\t86618\t96749\tU\t0\t0\n+chr1\t136956468\t136956598\tNM_026024_Ube2t\t+\t136857731\t136870739\t85729\t98737\t85729\tD\t0\t0\n+chr1\t136956468\t136956598\tNM_134438_Gpr37l1\t-\t137069087\t137054243\t97645\t112489\t97645\tD\t0\t0\n+chr1\t13829227\t13829564\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t138437726\t138437860\tNM_177643_Zfp281\t+\t138487073\t138526617\t49213\t49213\t88757\tU\t0\t0\n+chr1\t140381656\t140381785\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t145591041\t145591176\tNM_001038592_Glrx2\t+\t145585774\t145608282\t0\t5267\t17106\t.\t1\t0\n+chr1\t145591041\t145591176\tNM_019562_Uchl5\t+\t145623774\t145654586\t32598\t32598\t63410\tU\t0\t0\n+chr1\t145591041\t145591176\tNM_013835_Trove2\t-\t145624178\t145597816\t6640\t33002\t6640\tD\t0\t0\n+chr1\t145591041\t145591176\tNM_145991_Cdc73\t-\t145549936\t145274292\t41105\t41105\t316749\tU\t0\t0\n+chr1\t154971572\t154971673\tNM_008485_Lamc2\t-\t155033557\t154969890\t0\t61884\t1682\t.\t1\t0\n+chr1\t155123313\t155123435\tNM_010683_Lamc1\t-\t155179906\t155065803\t0\t56471\t57510\t.\t1\t0\n+chr1\t155123313\t155123435\tNM_008485_Lamc2\t-\t155033557\t154969890\t89756\t89756\t153423\tU\t0\t0\n+chr1\t158510523\t158510813\tNM_009230_Soat1\t-\t158417632\t158354679\t92891\t92891\t155844\tU\t0\t0\n+chr1\t158510523\t158510813\tNM_023141_Tor3a\t-\t158604477\t158583760\t72947\t93664\t72947\tD\t0\t0\n+chr1\t158537267\t158537411\tNM_023141_Tor3a\t-\t158604477\t158583760\t46349\t67066\t46349\tD\t0\t0\n+chr1\t158537267\t158537411\tNM_145413_Fam20b\t-\t158649180\t158608676\t71265\t111769\t71265\tD\t0\t0\n+chr1\t158537267\t158537411\tNM_009230_Soat1\t-\t158417632\t158354679\t119635\t119635\t182588\tU\t0\t0\n+chr1\t158580638\t158580759\tNM_023141_Tor3a\t-\t158604477\t158583760\t3001\t23718\t3001\tD\t0\t0\n+chr1\t158580638\t158580759\tNM_145413_Fam20b\t-\t158649180\t158608676\t27917\t68421\t27917\tD\t0\t0\n+chr1\t158835251\t158835391\tNM_028333_Angptl1\t+\t158769061\t158791209\t44042\t66190\t44042\tD\t0\t0\n+chr1\t159240736\t159240866\tBC055845_2810025M15Rik\t+\t159342483\t159350353\t101617\t101617\t109487\tU\t0\t0\n+chr1\t163827897\t163828062\tNM_026078_Pigc\t+\t163860747\t163957217\t32685\t32685\t129155\tU\t0\t0\n+chr1\t163827897\t163828062\tNM_010177_Fasl\t-\t163718844\t163710820\t109053\t109053\t117077\tU\t0\t0\n+chr1\t164215623\t164215935\tNR_002870_Dnm3os\t+\t16411'..b'1\t60929\tU\t0\t0\n+chr1\t44195449\t44195639\tNM_023645_Kdelc1\t-\t44177102\t44143458\t18347\t18347\t51991\tU\t0\t0\n+chr1\t44195449\t44195639\tNM_144558_Bivm\t+\t44175822\t44201615\t0\t19627\t5976\t.\t1\t0\n+chr1\t52625416\t52625560\tNM_008667_Nab1\t-\t52611216\t52487127\t14200\t14200\t138289\tU\t0\t0\n+chr1\t52625416\t52625560\tNM_001142647_Tmem194b\t+\t52687569\t52708760\t62009\t62009\t83200\tU\t0\t0\n+chr1\t54631692\t54631815\tENSMUST00000094950_Pgap1\t-\t54614539\t54529849\t17153\t17153\t101843\tU\t0\t0\n+chr1\t55283572\t55283675\tNM_028713_Rftn2\t-\t55283748\t55227030\t0\t73\t56542\t.\t1\t1\n+chr1\t55283572\t55283675\tNM_175439_Mars2\t+\t55294084\t55297625\t10409\t10409\t13950\tU\t0\t0\n+chr1\t55283572\t55283675\tNM_025283_Mobkl3\t+\t55187734\t55211736\t71836\t95838\t71836\tD\t0\t0\n+chr1\t63664888\t63665018\tNM_011780_Adam23\t+\t63640970\t63642850\t22038\t23918\t22038\tD\t0\t0\n+chr1\t63664888\t63665018\tNM_029696_Mdh1b\t-\t63776894\t63745401\t80383\t111876\t80383\tD\t0\t0\n+chr1\t63664888\t63665018\tNM_172422_Fastkd2\t+\t63777134\t63803028\t112116\t112116\t138010\tU\t0\t0\n+chr1\t72769824\t72770056\tNM_176980_Ankar\t-\t72747143\t72689581\t22681\t22681\t80243\tU\t0\t0\n+chr1\t72769824\t72770056\tNM_008342_Igfbp2\t+\t72840313\t72899038\t70257\t70257\t128982\tU\t0\t0\n+chr1\t72770058\t72770226\tNM_176980_Ankar\t-\t72747143\t72689581\t22915\t22915\t80477\tU\t0\t0\n+chr1\t72770058\t72770226\tNM_008342_Igfbp2\t+\t72840313\t72899038\t70087\t70087\t128812\tU\t0\t0\n+chr1\t72815517\t72815742\tNM_008342_Igfbp2\t+\t72840313\t72899038\t24571\t24571\t83296\tU\t0\t0\n+chr1\t72815517\t72815742\tNM_176980_Ankar\t-\t72747143\t72689581\t68374\t68374\t125936\tU\t0\t0\n+chr1\t72815517\t72815742\tNM_010518_Igfbp5\t-\t72921468\t72904507\t88765\t105726\t88765\tD\t0\t0\n+chr1\t75481920\t75482054\tNM_001001565_Chpf\t-\t75476437\t75470923\t5483\t5483\t10997\tU\t0\t0\n+chr1\t75481920\t75482054\tNM_178884_Obsl1\t-\t75503218\t75482401\t347\t21164\t347\tD\t0\t0\n+chr1\t75481920\t75482054\tNM_010564_Inha\t+\t75503647\t75506924\t21593\t21593\t24870\tU\t0\t0\n+chr1\t75481920\t75482054\tNM_183022_Accn4\t+\t75447063\t75470207\t11713\t34857\t11713\tD\t0\t0\n+chr1\t77457642\t77457791\tNM_007936_Epha4\t-\t77511653\t77280640\t0\t53862\t177002\t.\t1\t0\n+chr1\t78630893\t78631160\tNM_028817_Acsl3\t+\t78654388\t78743434\t23228\t23228\t112274\tU\t0\t0\n+chr1\t78630893\t78631160\tNM_011811_Farsb\t-\t78506689\t78414533\t124204\t124204\t216360\tU\t0\t0\n+chr1\t88408969\t88409267\tNM_172974_Cops7b\t+\t88478926\t88503950\t69659\t69659\t94683\tU\t0\t0\n+chr1\t88408969\t88409267\tNM_008801_Pde6d\t-\t88479102\t88427331\t18064\t69835\t18064\tD\t0\t0\n+chr1\t88408969\t88409267\tNM_010341_Nmur1\t-\t88297441\t88282479\t111528\t111528\t126490\tU\t0\t0\n+chr1\t89989553\t89989714\tNM_201641_Ugt1a10\t+\t89922380\t90115570\t0\t67173\t125856\t.\t1\t0\n+chr1\t89989553\t89989714\tNM_008299_Dnajb3\t-\t90102337\t90101307\t111593\t112623\t111593\tD\t0\t0\n+chr1\t90412932\t90413132\tNM_008132_Glrp1\t-\t90406631\t90396446\t6301\t6301\t16486\tU\t0\t0\n+chr1\t90412932\t90413132\tNM_029269_Spp2\t+\t90303568\t90373213\t39719\t109364\t39719\tD\t0\t0\n+chr1\t90592499\t90592629\tNM_177305_Arl4c\t-\t90617572\t90569702\t0\t24943\t22797\t.\t1\t0\n+chr1\t91496003\t91496145\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t91496155\t91496319\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t92070253\t92070431\tNM_007722_Cxcr7\t+\t92100063\t92112863\t29632\t29632\t42432\tU\t0\t0\n+chr1\t95186508\t95186637\tNM_178051_Mterfd2\t-\t95202630\t95195779\t9142\t15993\t9142\tD\t0\t0\n+chr1\t95186508\t95186637\tNM_023200_Ppp1r7\t+\t95239431\t95266345\t52794\t52794\t79708\tU\t0\t0\n+chr1\t95186508\t95186637\tNM_080850_Pask\t-\t95240039\t95205357\t18720\t53402\t18720\tD\t0\t0\n+chr1\t95186508\t95186637\tNM_172463_Sned1\t+\t95132418\t95197642\t0\t54090\t11005\t.\t1\t0\n+chr1\t9619046\t9619167\tNM_178399_3110035E14Rik\t+\t9591248\t9617222\t1824\t27798\t1824\tD\t0\t0\n+chr1\t9619046\t9619167\tNM_008651_Mybl1\t-\t9690280\t9635825\t16658\t71113\t16658\tD\t0\t0\n+chr1\t9619046\t9619167\tNM_175236_Adhfe1\t+\t9538049\t9570746\t48300\t80997\t48300\tD\t0\t0\n+chr1\t9619046\t9619167\tNM_021511_Rrs1\t+\t9535513\t9537532\t81514\t83533\t81514\tD\t0\t0\n+chr1\t9619175\t9619382\tNM_178399_3110035E14Rik\t+\t9591248\t9617222\t1953\t27927\t1953\tD\t0\t0\n+chr1\t9619175\t9619382\tNM_008651_Mybl1\t-\t9690280\t9635825\t16443\t70898\t16443\tD\t0\t0\n+chr1\t9619175\t9619382\tNM_175236_Adhfe1\t+\t9538049\t9570746\t48429\t81126\t48429\tD\t0\t0\n+chr1\t9619175\t9619382\tNM_021511_Rrs1\t+\t9535513\t9537532\t81643\t83662\t81643\tD\t0\t0\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/features_per_peak3.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_per_peak3.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| @@ -0,0 +1,70 @@ +#peak.chr peak.start peak.end gene.id_1 strand_1 TSS_1 TES_1 dist_closest_1 dist_TSS_1 dist_TES_1 direction_1 overlap_gene_1 overlap_promoter_1 gene.id_2 strand_2 TSS_2 TES_2 dist_closest_2 dist_TSS_2 dist_TES_2 direction_2 overlap_gene_2 overlap_promoter_2 gene.id_3 strand_3 TSS_3 TES_3 dist_closest_3 dist_TSS_3 dist_TES_3 direction_3 overlap_gene_3 overlap_promoter_3 gene.id_4 strand_4 TSS_4 TES_4 dist_closest_4 dist_TSS_4 dist_TES_4 direction_4 overlap_gene_4 overlap_promoter_4 +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 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . +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 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . +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 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . +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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/features_per_peak4.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_per_peak4.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,277 @@\n+#peak.chr\tpeak.start\tpeak.end\tgene.id\tstrand\tTSS\tTES\tdist_closest\tdist_TSS\tdist_TES\tdirection\toverlap_gene\toverlap_promoter\n+chr1\t10617233\t10617437\tNM_177834_Cpa6\t-\t10710026\t10314801\t0\t92589\t302432\t.\t1\t0\n+chr1\t10617233\t10617437\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t10617233\t10617437\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t10617233\t10617437\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t108747519\t108747791\tNM_009190_Vps4b\t-\t108739123\t108665873\t8396\t8396\t81646\tU\t0\t0\n+chr1\t108747519\t108747791\tNM_009257_Serpinb5\t+\t108757652\t108779925\t9861\t9861\t32134\tU\t0\t0\n+chr1\t108747519\t108747791\tNM_027971_Serpinb12\t+\t108831026\t108853655\t83235\t83235\t105864\tU\t0\t0\n+chr1\t108747519\t108747791\tNM_027534_Kdsr\t-\t108656357\t108617007\t91162\t91162\t130512\tU\t0\t0\n+chr1\t120760212\t120760461\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t120760212\t120760461\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t120760212\t120760461\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t120760212\t120760461\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t132950929\t132951247\tNM_010548_Il10\t+\t132916424\t132921547\t29382\t34505\t29382\tD\t0\t0\n+chr1\t132950929\t132951247\tNM_001009940_Il19\t-\t132915234\t132786042\t35695\t35695\t164887\tU\t0\t0\n+chr1\t132950929\t132951247\tNM_008551_Mapkapk2\t-\t133013820\t132950274\t0\t62573\t655\t.\t1\t0\n+chr1\t132950929\t132951247\tNM_145508_Dyrk3\t-\t133034897\t133018921\t67674\t83650\t67674\tD\t0\t0\n+chr1\t133114860\t133115015\tNM_018750_Rassf5\t-\t133144761\t133072991\t0\t29746\t41869\t.\t1\t0\n+chr1\t133114860\t133115015\tNM_019777_Ikbke\t-\t133176163\t133151052\t36037\t61148\t36037\tD\t0\t0\n+chr1\t133114860\t133115015\tNM_001136070_Lgtn\t+\t133049773\t133084235\t30625\t65087\t30625\tD\t0\t0\n+chr1\t133114860\t133115015\tNM_145508_Dyrk3\t-\t133034897\t133018921\t79963\t79963\t95939\tU\t0\t0\n+chr1\t135582677\t135582828\tNM_001159649_Lax1\t-\t135586665\t135575626\t0\t3837\t7051\t.\t1\t0\n+chr1\t135582677\t135582828\tNM_144530_Zc3h11a\t-\t135557956\t135516445\t24721\t24721\t66232\tU\t0\t0\n+chr1\t135582677\t135582828\tNM_213616_Atp2b4\t-\t135697538\t135602265\t19437\t114710\t19437\tD\t0\t0\n+chr1\t135582677\t135582828\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t135851853\t135852218\tNM_054077_Prelp\t-\t135865173\t135806855\t0\t12955\t44998\t.\t1\t0\n+chr1\t135851853\t135852218\tNM_054076_Optc\t-\t135805299\t135787973\t46554\t46554\t63880\tU\t0\t0\n+chr1\t135851853\t135852218\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t135851853\t135852218\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t136956468\t136956598\tNM_007955_Ptprv\t-\t137029151\t137004306\t47708\t72553\t47708\tD\t0\t0\n+chr1\t136956468\t136956598\tNM_026823_Arl8a\t+\t137043216\t137053347\t86618\t86618\t96749\tU\t0\t0\n+chr1\t136956468\t136956598\tNM_026024_Ube2t\t+\t136857731\t136870739\t85729\t98737\t85729\tD\t0\t0\n+chr1\t136956468\t136956598\tNM_134438_Gpr37l1\t-\t137069087\t137054243\t97645\t112489\t97645\tD\t0\t0\n+chr1\t13829227\t13829564\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t13829227\t13829564\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t13829227\t13829564\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t13829227\t13829564\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t138437726\t138437860\tNM_177643_Zfp281\t+\t138487073\t138526617\t49213\t49213\t88757\tU\t0\t0\n+chr1\t138437726\t138437860\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t138437726\t138437860\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t138437726\t138437860\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t140381656\t140381785\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t140381656\t140381785\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t140381656\t140381785\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t140381656\t140381785\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t145591041\t145591176\tNM_001038592_Glrx2\t+\t145585774\t145608282\t0\t5267\t17106\t.\t1\t0\n+chr1\t145591041\t145591176\tNM_019562_Uchl5\t+\t145623774\t145654586\t32598\t32598\t63410\tU\t0\t0\n+chr1\t145591041\t145591176\tNM_013835_Trove2\t-\t145624178\t145597816\t6640\t33002\t6640\tD\t0\t0\n+chr1\t145591041\t145591176\tNM_145991_Cdc73\t-\t145549936\t145274292\t41105\t41105\t316749\tU\t0\t0\n+chr1\t154971572\t154971673\tNM_008485_Lamc2\t-\t155033557\t154969890\t0\t61884\t1682\t.\t1\t0\n+chr1\t154971572\t154971673\t---\t---\t'..b'17\t72815742\tNM_010518_Igfbp5\t-\t72921468\t72904507\t88765\t105726\t88765\tD\t0\t0\n+chr1\t72815517\t72815742\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t75481920\t75482054\tNM_001001565_Chpf\t-\t75476437\t75470923\t5483\t5483\t10997\tU\t0\t0\n+chr1\t75481920\t75482054\tNM_178884_Obsl1\t-\t75503218\t75482401\t347\t21164\t347\tD\t0\t0\n+chr1\t75481920\t75482054\tNM_010564_Inha\t+\t75503647\t75506924\t21593\t21593\t24870\tU\t0\t0\n+chr1\t75481920\t75482054\tNM_183022_Accn4\t+\t75447063\t75470207\t11713\t34857\t11713\tD\t0\t0\n+chr1\t77457642\t77457791\tNM_007936_Epha4\t-\t77511653\t77280640\t0\t53862\t177002\t.\t1\t0\n+chr1\t77457642\t77457791\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t77457642\t77457791\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t77457642\t77457791\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t78630893\t78631160\tNM_028817_Acsl3\t+\t78654388\t78743434\t23228\t23228\t112274\tU\t0\t0\n+chr1\t78630893\t78631160\tNM_011811_Farsb\t-\t78506689\t78414533\t124204\t124204\t216360\tU\t0\t0\n+chr1\t78630893\t78631160\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t78630893\t78631160\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t88408969\t88409267\tNM_172974_Cops7b\t+\t88478926\t88503950\t69659\t69659\t94683\tU\t0\t0\n+chr1\t88408969\t88409267\tNM_008801_Pde6d\t-\t88479102\t88427331\t18064\t69835\t18064\tD\t0\t0\n+chr1\t88408969\t88409267\tNM_010341_Nmur1\t-\t88297441\t88282479\t111528\t111528\t126490\tU\t0\t0\n+chr1\t88408969\t88409267\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t89989553\t89989714\tNM_201641_Ugt1a10\t+\t89922380\t90115570\t0\t67173\t125856\t.\t1\t0\n+chr1\t89989553\t89989714\tNM_008299_Dnajb3\t-\t90102337\t90101307\t111593\t112623\t111593\tD\t0\t0\n+chr1\t89989553\t89989714\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t89989553\t89989714\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t90412932\t90413132\tNM_008132_Glrp1\t-\t90406631\t90396446\t6301\t6301\t16486\tU\t0\t0\n+chr1\t90412932\t90413132\tNM_029269_Spp2\t+\t90303568\t90373213\t39719\t109364\t39719\tD\t0\t0\n+chr1\t90412932\t90413132\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t90412932\t90413132\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t90592499\t90592629\tNM_177305_Arl4c\t-\t90617572\t90569702\t0\t24943\t22797\t.\t1\t0\n+chr1\t90592499\t90592629\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t90592499\t90592629\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t90592499\t90592629\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t91496003\t91496145\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t91496003\t91496145\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t91496003\t91496145\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t91496003\t91496145\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t91496155\t91496319\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t91496155\t91496319\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t91496155\t91496319\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t91496155\t91496319\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t92070253\t92070431\tNM_007722_Cxcr7\t+\t92100063\t92112863\t29632\t29632\t42432\tU\t0\t0\n+chr1\t92070253\t92070431\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t92070253\t92070431\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t92070253\t92070431\t---\t---\t---\t---\t---\t---\t---\t---\t---\t---\n+chr1\t95186508\t95186637\tNM_178051_Mterfd2\t-\t95202630\t95195779\t9142\t15993\t9142\tD\t0\t0\n+chr1\t95186508\t95186637\tNM_023200_Ppp1r7\t+\t95239431\t95266345\t52794\t52794\t79708\tU\t0\t0\n+chr1\t95186508\t95186637\tNM_080850_Pask\t-\t95240039\t95205357\t18720\t53402\t18720\tD\t0\t0\n+chr1\t95186508\t95186637\tNM_172463_Sned1\t+\t95132418\t95197642\t0\t54090\t11005\t.\t1\t0\n+chr1\t9619046\t9619167\tNM_178399_3110035E14Rik\t+\t9591248\t9617222\t1824\t27798\t1824\tD\t0\t0\n+chr1\t9619046\t9619167\tNM_008651_Mybl1\t-\t9690280\t9635825\t16658\t71113\t16658\tD\t0\t0\n+chr1\t9619046\t9619167\tNM_175236_Adhfe1\t+\t9538049\t9570746\t48300\t80997\t48300\tD\t0\t0\n+chr1\t9619046\t9619167\tNM_021511_Rrs1\t+\t9535513\t9537532\t81514\t83533\t81514\tD\t0\t0\n+chr1\t9619175\t9619382\tNM_178399_3110035E14Rik\t+\t9591248\t9617222\t1953\t27927\t1953\tD\t0\t0\n+chr1\t9619175\t9619382\tNM_008651_Mybl1\t-\t9690280\t9635825\t16443\t70898\t16443\tD\t0\t0\n+chr1\t9619175\t9619382\tNM_175236_Adhfe1\t+\t9538049\t9570746\t48429\t81126\t48429\tD\t0\t0\n+chr1\t9619175\t9619382\tNM_021511_Rrs1\t+\t9535513\t9537532\t81643\t83662\t81643\tD\t0\t0\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/features_per_peak4.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/features_per_peak4.summary Wed Feb 24 09:39:14 2016 -0500 |
| b |
| @@ -0,0 +1,70 @@ +#peak.chr peak.start peak.end gene.id strand TSS TES dist_closest dist_TSS dist_TES direction overlap_gene overlap_promoter +chr1 10617233 10617437 NM_177834_Cpa6 - 10710026 10314801 0 92589 302432 . 1 0 +chr1 108747519 108747791 NM_009190_Vps4b - 108739123 108665873 8396 8396 81646 U 0 0 +chr1 120760212 120760461 --- --- --- --- --- --- --- --- --- --- +chr1 132950929 132951247 NM_010548_Il10 + 132916424 132921547 29382 34505 29382 D 0 0 +chr1 133114860 133115015 NM_018750_Rassf5 - 133144761 133072991 0 29746 41869 . 1 0 +chr1 135582677 135582828 NM_001159649_Lax1 - 135586665 135575626 0 3837 7051 . 1 0 +chr1 135851853 135852218 NM_054077_Prelp - 135865173 135806855 0 12955 44998 . 1 0 +chr1 136956468 136956598 NM_007955_Ptprv - 137029151 137004306 47708 72553 47708 D 0 0 +chr1 13829227 13829564 --- --- --- --- --- --- --- --- --- --- +chr1 138437726 138437860 NM_177643_Zfp281 + 138487073 138526617 49213 49213 88757 U 0 0 +chr1 140381656 140381785 --- --- --- --- --- --- --- --- --- --- +chr1 145591041 145591176 NM_001038592_Glrx2 + 145585774 145608282 0 5267 17106 . 1 0 +chr1 154971572 154971673 NM_008485_Lamc2 - 155033557 154969890 0 61884 1682 . 1 0 +chr1 155123313 155123435 NM_010683_Lamc1 - 155179906 155065803 0 56471 57510 . 1 0 +chr1 158510523 158510813 NM_009230_Soat1 - 158417632 158354679 92891 92891 155844 U 0 0 +chr1 158537267 158537411 NM_023141_Tor3a - 158604477 158583760 46349 67066 46349 D 0 0 +chr1 158580638 158580759 NM_023141_Tor3a - 158604477 158583760 3001 23718 3001 D 0 0 +chr1 158835251 158835391 NM_028333_Angptl1 + 158769061 158791209 44042 66190 44042 D 0 0 +chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 U 0 0 +chr1 163827897 163828062 NM_026078_Pigc + 163860747 163957217 32685 32685 129155 U 0 0 +chr1 164215623 164215935 NR_002870_Dnm3os + 164119785 164155671 59952 95838 59952 D 0 0 +chr1 167222964 167223261 NM_145513_Tiprl - 167183116 167133855 39848 39848 89109 U 0 0 +chr1 167906284 167906554 NM_198934_Pou2f1 - 167932753 167804181 0 26199 102103 . 1 0 +chr1 170255081 170255260 --- --- --- --- --- --- --- --- --- --- +chr1 17030405 17030545 NM_020604_Jph1 - 17087942 16837549 0 57397 192856 . 1 0 +chr1 172620779 172620912 NM_177068_Olfml2b + 172569075 172612915 7864 51704 7864 D 0 0 +chr1 172620917 172621080 NM_177068_Olfml2b + 172569075 172612915 8002 51842 8002 D 0 0 +chr1 174376470 174376659 NM_029612_Slamf9 + 174392516 174408706 15857 15857 32047 U 0 0 +chr1 181061299 181061446 --- --- --- --- --- --- --- --- --- --- +chr1 182479646 182479905 NM_007415_Parp1 + 182499033 182531385 19128 19128 51480 U 0 0 +chr1 185854947 185855105 NM_022019_Dusp10 + 185755009 185899515 0 99938 44410 . 1 0 +chr1 194258648 194259032 --- --- --- --- --- --- --- --- --- --- +chr1 194645118 194645475 NM_144881_Hhat - 194649833 194320603 0 4358 324515 . 1 0 +chr1 194957396 194957723 NM_145415_AA408296 - 194956446 194918802 950 950 38594 U 0 1 +chr1 195324443 195324741 NM_144817_Camk1g - 195216632 195172540 107811 107811 151903 U 0 0 +chr1 195330701 195330930 NM_144817_Camk1g - 195216632 195172540 114069 114069 158161 U 0 0 +chr1 195338316 195338616 NM_144817_Camk1g - 195216632 195172540 121684 121684 165776 U 0 0 +chr1 195342728 195342985 NM_144817_Camk1g - 195216632 195172540 126096 126096 170188 U 0 0 +chr1 195384767 195385195 --- --- --- --- --- --- --- --- --- --- +chr1 197057796 197057843 NM_007758_Cr2 - 197003002 196963005 54794 54794 94791 U 0 0 +chr1 24609562 24609623 NM_007733_Col19a1 - 24602262 24258667 7300 7300 350895 U 0 0 +chr1 24609923 24609992 NM_007733_Col19a1 - 24602262 24258667 7661 7661 351256 U 0 0 +chr1 24730996 24731077 NM_026719_Lmbrd1 + 24820582 24823143 89505 89505 92066 U 0 0 +chr1 26734195 26734485 --- --- --- --- --- --- --- --- --- --- +chr1 34206924 34207100 --- --- --- --- --- --- --- --- --- --- +chr1 36106813 36107058 NM_015818_Hs6st1 + 36125255 36163289 18197 18197 56231 U 0 0 +chr1 39492140 39492513 NM_018775_Tbc1d8 - 39544345 39428350 0 51832 63790 . 1 0 +chr1 40325917 40326123 NM_008362_Il1r1 + 40274145 40373439 0 51772 47316 . 1 0 +chr1 44195449 44195639 NM_011729_Ercc5 + 44204270 44256568 8631 8631 60929 U 0 0 +chr1 52625416 52625560 NM_008667_Nab1 - 52611216 52487127 14200 14200 138289 U 0 0 +chr1 54631692 54631815 ENSMUST00000094950_Pgap1 - 54614539 54529849 17153 17153 101843 U 0 0 +chr1 55283572 55283675 NM_028713_Rftn2 - 55283748 55227030 0 73 56542 . 1 1 +chr1 63664888 63665018 NM_011780_Adam23 + 63640970 63642850 22038 23918 22038 D 0 0 +chr1 72769824 72770056 NM_176980_Ankar - 72747143 72689581 22681 22681 80243 U 0 0 +chr1 72770058 72770226 NM_176980_Ankar - 72747143 72689581 22915 22915 80477 U 0 0 +chr1 72815517 72815742 NM_008342_Igfbp2 + 72840313 72899038 24571 24571 83296 U 0 0 +chr1 75481920 75482054 NM_001001565_Chpf - 75476437 75470923 5483 5483 10997 U 0 0 +chr1 77457642 77457791 NM_007936_Epha4 - 77511653 77280640 0 53862 177002 . 1 0 +chr1 78630893 78631160 NM_028817_Acsl3 + 78654388 78743434 23228 23228 112274 U 0 0 +chr1 88408969 88409267 NM_172974_Cops7b + 88478926 88503950 69659 69659 94683 U 0 0 +chr1 89989553 89989714 NM_201641_Ugt1a10 + 89922380 90115570 0 67173 125856 . 1 0 +chr1 90412932 90413132 NM_008132_Glrp1 - 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|
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_features_per_peak.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_features_per_peak.out Wed Feb 24 09:39:14 2016 -0500 |
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| b'@@ -0,0 +1,502 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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_features_per_peak1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_features_per_peak1.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,501 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|
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_features_per_peak3.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_features_per_peak3.out Wed Feb 24 09:39:14 2016 -0500 |
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| b'@@ -0,0 +1,2001 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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_features_per_peak3.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_features_per_peak3.summary Wed Feb 24 09:39:14 2016 -0500 |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_features_per_peak_compact.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_features_per_peak_compact.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,501 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|
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_features_per_summit.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_features_per_summit.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,501 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t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t13179280\t13179281\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t13934524\t13934525\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t14479277\t14479278\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.'..b'\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t148900032\t148900033\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t148988309\t148988310\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t149151516\t149151517\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t149373423\t149373424\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t149547172\t149547173\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t149930099\t149930100\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t150523771\t150523772\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t151852781\t151852782\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t151941991\t151941992\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t152055844\t152055845\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t152768992\t152768993\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t153117376\t153117377\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t153562593\t153562594\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t153617551\t153617552\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t154259255\t154259256\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t154305193\t154305194\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t154793310\t154793311\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t154959021\t154959022\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t155608292\t155608293\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t155676641\t155676642\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t155882149\t155882150\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t156957961\t156957962\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157054389\t157054390\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157229460\t157229461\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157232537\t157232538\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157353367\t157353368\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157530064\t157530065\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157616665\t157616666\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157708175\t157708176\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157854160\t157854161\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157916567\t157916568\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t157960555\t157960556\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158166030\t158166031\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158365460\t158365461\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t158890212\t158890213\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t159139993\t159139994\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+chr1\t159875548\t159875549\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n' 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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_peaks1.xlsx |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_peaks3.xlsx |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_peaks_compact.xls |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_peaks_per_feature.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_peaks_per_feature.out Wed Feb 24 09:39:14 2016 -0500 |
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| @@ -0,0 +1,10 @@ +#gene.id gene.chr gene.start gene.end gene.strand peak.chr peak.start peak.end order dist_closest dist_TSS dist_TES +Xkr4 chr1 3204562 3661579 - chr1 3621547 3621583 1 of 1 0 39996 416985 +AK149000 chr1 3638391 3648985 - chr1 3621547 3621583 1 of 1 16808 27402 16808 +Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- --- +Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- --- +Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- --- +Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- --- +Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- --- +Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- --- +Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- --- |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_peaks_per_feature1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_peaks_per_feature1.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| @@ -0,0 +1,10 @@ +#gene.id gene.chr gene.start gene.end gene.strand chr_1 start_1 end_1 dist_closest_1 dist_TSS_1 direction_1 in_the_gene_1 chr_2 start_2 end_2 dist_closest_2 dist_TSS_2 direction_2 in_the_gene_2 chr_3 start_3 end_3 dist_closest_3 dist_TSS_3 direction_3 in_the_gene_3 chr_4 start_4 end_4 dist_closest_4 dist_TSS_4 direction_4 in_the_gene_4 +Xkr4 chr1 3204562 3661579 - chr1 3621547 3621583 0 39996 . YES . . . . . . . . . . . . . . . . . . . . . +AK149000 chr1 3638391 3648985 - chr1 3621547 3621583 16808 27402 U NO . . . . . . . . . . . . . . . . . . . . . +Rp1 chr1 4333587 4350395 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Sox17 chr1 4481008 4486494 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Mrpl15 chr1 4763278 4775807 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Lypla1 chr1 4797973 4836816 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Tcea1 chr1 4847774 4887990 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Rgs20 chr1 4899656 5060366 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Atp6v1h chr1 5073253 5152630 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_peaks_per_feature3.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_peaks_per_feature3.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| @@ -0,0 +1,37 @@ +#gene.id gene.chr gene.start gene.end gene.strand chr start end dist_closest dist_TSS direction in_the_gene +Xkr4 chr1 3204562 3661579 - chr1 3621547 3621583 0 39996 . YES +Xkr4 chr1 3204562 3661579 - --- --- --- --- --- --- --- +Xkr4 chr1 3204562 3661579 - --- --- --- --- --- --- --- +Xkr4 chr1 3204562 3661579 - --- --- --- --- --- --- --- +AK149000 chr1 3638391 3648985 - chr1 3621547 3621583 16808 27402 U NO +AK149000 chr1 3638391 3648985 - --- --- --- --- --- --- --- +AK149000 chr1 3638391 3648985 - --- --- --- --- --- --- --- +AK149000 chr1 3638391 3648985 - --- --- --- --- --- --- --- +Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- --- +Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- --- +Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- --- +Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- --- +Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- --- +Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- --- +Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- --- +Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- --- +Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- --- +Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- --- +Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- --- +Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- --- +Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- --- +Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- --- +Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- --- +Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- --- +Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- --- +Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- --- +Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- --- +Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- --- +Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- --- +Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- --- +Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- --- +Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- --- +Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- --- +Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- --- +Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- --- +Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- --- |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_peaks_per_feature3.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_peaks_per_feature3.summary Wed Feb 24 09:39:14 2016 -0500 |
| b |
| @@ -0,0 +1,10 @@ +#gene.id gene.chr gene.start gene.end gene.strand chr start end dist_closest dist_TSS direction in_the_gene +Xkr4 chr1 3204562 3661579 - chr1 3621547 3621583 0 39996 . YES +AK149000 chr1 3638391 3648985 - chr1 3621547 3621583 16808 27402 U NO +Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- --- +Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- --- +Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- --- +Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- --- +Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- --- +Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- --- +Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- --- |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_peaks_per_feature_compact.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_peaks_per_feature_compact.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| @@ -0,0 +1,10 @@ +#gene.id chr_1 start_1 end_1 dist_closest_1 direction_1 chr_2 start_2 end_2 dist_closest_2 direction_2 chr_3 start_3 end_3 dist_closest_3 direction_3 chr_4 start_4 end_4 dist_closest_4 direction_4 +Xkr4 chr1 3621547 3621583 0 . . . . . . . . . . . . . . . . +AK149000 chr1 3621547 3621583 16808 U . . . . . . . . . . . . . . . +Rp1 . . . . . . . . . . . . . . . . . . . . +Sox17 . . . . . . . . . . . . . . . . . . . . +Mrpl15 . . . . . . . . . . . . . . . . . . . . +Lypla1 . . . . . . . . . . . . . . . . . . . . +Tcea1 . . . . . . . . . . . . . . . . . . . . +Rgs20 . . . . . . . . . . . . . . . . . . . . +Atp6v1h . . . . . . . . . . . . . . . . . . . . |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_summits.xls |
| b |
| Binary file test-data/mm9_summits.xls has changed |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_summits.xlsx |
| b |
| Binary file test-data/mm9_summits.xlsx has changed |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_summits_per_feature.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm9_summits_per_feature.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| @@ -0,0 +1,10 @@ +#gene.id gene.chr gene.start gene.end gene.strand chr_1 start_1 end_1 dist_closest_1 dist_TSS_1 direction_1 in_the_gene_1 chr_2 start_2 end_2 dist_closest_2 dist_TSS_2 direction_2 in_the_gene_2 chr_3 start_3 end_3 dist_closest_3 dist_TSS_3 direction_3 in_the_gene_3 chr_4 start_4 end_4 dist_closest_4 dist_TSS_4 direction_4 in_the_gene_4 +Xkr4 chr1 3204562 3661579 - chr1 3621547 3621548 0 40031 . YES . . . . . . . . . . . . . . . . . . . . . +AK149000 chr1 3638391 3648985 - chr1 3621547 3621548 16843 27437 U NO . . . . . . . . . . . . . . . . . . . . . +Rp1 chr1 4333587 4350395 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Sox17 chr1 4481008 4486494 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Mrpl15 chr1 4763278 4775807 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Lypla1 chr1 4797973 4836816 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Tcea1 chr1 4847774 4887990 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Rgs20 chr1 4899656 5060366 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +Atp6v1h chr1 5073253 5152630 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_summits_to_transcripts.out --- a/test-data/mm9_summits_to_transcripts.out Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -#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 --- --- --- |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_transcripts_to_edges.out --- a/test-data/mm9_transcripts_to_edges.out Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -#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 |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_transcripts_to_edges.summary --- a/test-data/mm9_transcripts_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -#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 |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_tss_to_edges.out --- a/test-data/mm9_tss_to_edges.out Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -#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 |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_tss_to_edges.summary --- a/test-data/mm9_tss_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -#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 |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/mm9_tss_to_summits.out --- a/test-data/mm9_tss_to_summits.out Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,504 +0,0 @@\n-#chr\tstart\tgeneID\tnearest\tTSS\tdistance_to_TSS\tdistance_to_TES\tstrand\tin_the_gene\ttranscripts_inbetween\ttranscript_ids_inbetween\n-chr1\t3213477\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t3542857\tAK149000\t1 of 2\t3648985\t106128\t95534\t-\tNO\t0\t\n-chr1\t3542857\tXkr4\t2 of 2\t3661579\t118722\t-338295\t-\tYES\t1\tAK149000\n-chr1\t3560979\tAK149000\t1 of 2\t3648985\t88006\t77412\t-\tNO\t0\t\n-chr1\t3560979\tXkr4\t2 of 2\t3661579\t100600\t-356417\t-\tYES\t1\tAK149000\n-chr1\t3621547\tAK149000\t1 of 2\t3648985\t27438\t16844\t-\tNO\t0\t\n-chr1\t3621547\tXkr4\t2 of 2\t3661579\t40032\t-416985\t-\tYES\t1\tAK149000\n-chr1\t4630453\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t5261737\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t5562257\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t6926999\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t7262846\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t7322487\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t7666187\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t7744070\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t7969291\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t8421057\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t8679021\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t9359611\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t9415439\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t9608130\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t9616803\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t9897397\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t10251725\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t10254195\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t10305254\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t10451286\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t11340573\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t11610483\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t11960381\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t11987310\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t12441678\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t12704380\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t12871650\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t13179280\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t13934524\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t14479277\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t14755996\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t14848637\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t14967919\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t15097029\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t17128114\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t17160496\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t17334281\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t17605285\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t17922903\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t18681561\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t19213304\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t20317581\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t21466434\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t22074908\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t22696516\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t23655828\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t24583893\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t24738828\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t24743796\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t25009857\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t25313509\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t26503310\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t27025916\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t27385857\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t27598627\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t27636264\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t27687524\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t28357424\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t29135026\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t29633575\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t29825940\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t30137793\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t30142141\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t30465754\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t30785908\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t31077695\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t31123645\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t31158742\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t31883682\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t31990075\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t33079863\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t33288587\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t33856089\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t34588477\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t34633149\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t34749000\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t34764419\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t35032286\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t35047073\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t35933401\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t36135485\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t36742521\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t36859752\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t37388614\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t37763263\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t37824535\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t37974386\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t37994576\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t38460553\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t38502464\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t38761349\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t38832604\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t39388554\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t39439044\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t39593773\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t39693273\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t39924300\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t40132160\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t40243823\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t40426457\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t40773529\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t40785687\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t40953366\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t41021129\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t41080072\t.\t.\t.\t.\t.\t.\t.\t.\t.'..b'12\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t126963082\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t127190153\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t127228396\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t127507342\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t127703188\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t127735504\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t128049231\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t128388917\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t128791747\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t129571914\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t129582844\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t130923911\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t131245002\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t131624212\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t131653028\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t131673494\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t131762457\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t132812150\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t133122490\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t133337646\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t134107973\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t134516117\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t134650852\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t135304596\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t135346221\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t135595351\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t135645557\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t135794196\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t135833373\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t136109219\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t136151385\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t136219228\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t136276302\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t136409892\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t136846450\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t137021089\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t137057829\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t137256872\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t137292997\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t137340715\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t137563013\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t138237818\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t138288739\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t138701415\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t138883160\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t139093105\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t139286502\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t139448680\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t139944056\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t140207040\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t141517452\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t142087663\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t142561476\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t142732555\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t142765329\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t142811575\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t142823331\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t142985887\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t143071919\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t143137676\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t143684082\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t143803869\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t143866547\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t144585588\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t145018626\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t145169340\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t145286043\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t145743816\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t145793073\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t145943835\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t145973347\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t146233793\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t146349912\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t146992848\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t147015972\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t147919367\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t148073000\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t148184896\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t148571263\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t148727077\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t148900032\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t148988309\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t149151516\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t149373423\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t149547172\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t149930099\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t150523771\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t151852781\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t151941991\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t152055844\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t152768992\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t153117376\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t153562593\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t153617551\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t154259255\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t154305193\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t154793310\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t154959021\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t155608292\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t155676641\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t155882149\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t156957961\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157054389\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157229460\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157232537\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157353367\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157530064\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157616665\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157708175\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157854160\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157916567\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t157960555\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t158166030\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t158365460\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t158890212\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t159139993\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t159875548\t.\t.\t.\t.\t.\t.\t.\t.\t.\n' 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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/peaks.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks.txt Wed Feb 24 09:39:14 2016 -0500 |
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| @@ -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 |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/peaks2.xlsx |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/peaks3.xlsx |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/peaks_per_feature1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks_per_feature1.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,957 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5671\t+\tchr1\t164215623\t164215935\t59952\t95838\tU\tNO\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NR_003623_EG277333\tchr1\t182251970\t182262902\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NR_026896_4931440L10Rik\tchr1\t136437533\t136449760\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/peaks_per_feature2.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks_per_feature2.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,980 @@\n+#gene.id\tgene.chr\tgene.start\tgene.end\tgene.strand\tchr\tstart\tend\tdist_closest\tdist_TSS\tdirection\tin_the_gene\n+AF064749_Col6a3\tchr1\t92566771\t92800755\t-\t---\t---\t---\t---\t---\t---\t---\n+AK015559_4930472D16Rik\tchr1\t25020851\t25021989\t-\t---\t---\t---\t---\t---\t---\t---\n+AK030377_A330023F24Rik\tchr1\t196781953\t196826186\t-\t---\t---\t---\t---\t---\t---\t---\n+AK080193_A530079E22Rik\tchr1\t89401837\t89403491\t-\t---\t---\t---\t---\t---\t---\t---\n+AK082264_C230030N03Rik\tchr1\t34735043\t34781084\t+\t---\t---\t---\t---\t---\t---\t---\n+BC006931_AI597479\tchr1\t43153807\t43172843\t+\t---\t---\t---\t---\t---\t---\t---\n+BC021773_Glb1l\tchr1\t75193364\t75207353\t-\t---\t---\t---\t---\t---\t---\t---\n+BC023951_D1Ertd622e\tchr1\t99540054\t99558631\t-\t---\t---\t---\t---\t---\t---\t---\n+BC028767_3110009E18Rik\tchr1\t122017764\t122114603\t+\t---\t---\t---\t---\t---\t---\t---\n+BC031781_BC031781\tchr1\t182781250\t182798240\t+\t---\t---\t---\t---\t---\t---\t---\n+BC034187_BC035947\tchr1\t78493611\t78497758\t-\t---\t---\t---\t---\t---\t---\t---\n+BC043098_Fam168b\tchr1\t34870072\t34917183\t-\t---\t---\t---\t---\t---\t---\t---\n+BC049091_D1Bwg0212e\tchr1\t39592545\t39603734\t+\tchr1\t39492140\t39492513\t100032\t100032\tD\tNO\n+BC049713_Ankrd45\tchr1\t163072817\t163099826\t+\t---\t---\t---\t---\t---\t---\t---\n+BC050813_4921511C04Rik\tchr1\t37157481\t37244861\t+\t---\t---\t---\t---\t---\t---\t---\n+BC051128_4921521F21Rik\tchr1\t65059273\t65079312\t-\t---\t---\t---\t---\t---\t---\t---\n+BC052693_2810422O20Rik\tchr1\t165924541\t165927371\t+\t---\t---\t---\t---\t---\t---\t---\n+BC052931_A630001G21Rik\tchr1\t87601462\t87674840\t-\t---\t---\t---\t---\t---\t---\t---\n+BC053100_5730559C18Rik\tchr1\t138110108\t138130841\t-\t---\t---\t---\t---\t---\t---\t---\n+BC054802_9630058J23Rik\tchr1\t181476521\t181558044\t+\t---\t---\t---\t---\t---\t---\t---\n+BC055845_2810025M15Rik\tchr1\t159342483\t159350353\t+\tchr1\t159240736\t159240866\t101617\t101617\tD\tNO\n+BC055955_A130010J15Rik\tchr1\t194999663\t195004015\t+\tchr1\t194957396\t194957723\t41940\t41940\tD\tNO\n+BC057872_Rab3gap2\tchr1\t187028006\t187110623\t+\t---\t---\t---\t---\t---\t---\t---\n+BC058417_2610017I09Rik\tchr1\t42648822\t42751667\t-\t---\t---\t---\t---\t---\t---\t---\n+BC059254_Phlpp\tchr1\t108042052\t108306367\t+\t---\t---\t---\t---\t---\t---\t---\n+BC070435_Fam123c\tchr1\t34620070\t34671545\t+\t---\t---\t---\t---\t---\t---\t---\n+BC070446_Fam135a\tchr1\t24017617\t24107170\t-\t---\t---\t---\t---\t---\t---\t---\n+BC071241_9430016H08Rik\tchr1\t57463192\t57497936\t+\t---\t---\t---\t---\t---\t---\t---\n+BC072639_2010300C02Rik\tchr1\t37646877\t37776659\t-\t---\t---\t---\t---\t---\t---\t---\n+BC080290_5033414K04Rik\tchr1\t84032539\t84360735\t-\t---\t---\t---\t---\t---\t---\t---\n+BC082310_9430031J16Rik\tchr1\t81073525\t81338329\t+\t---\t---\t---\t---\t---\t---\t---\n+BC089525_2310007B03Rik\tchr1\t95047933\t95063386\t-\tchr1\t95186508\t95186637\t123122\t123122\tD\tNO\n+BC089561_Cep350\tchr1\t157692096\t157820375\t-\t---\t---\t---\t---\t---\t---\t---\n+BC147491_A230074B11Rik\tchr1\t37083441\t37133840\t+\t---\t---\t---\t---\t---\t---\t---\n+BC147657_9630028B13Rik\tchr1\t187253234\t187265698\t-\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000027997_Rgs5\tchr1\t171625108\t171625913\t+\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000051203_1700001G17Rik\tchr1\t33726669\t33727551\t+\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000054333_A130050O07Rik\tchr1\t139823828\t139826840\t+\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000056879_C230029F24Rik\tchr1\t49301475\t49397265\t+\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000057543_A730013G03Rik\tchr1\t194659323\t194661397\t-\tchr1\t194645118\t194645475\t13848\t15922\tU\tNO\n+ENSMUST00000062637_4930470H14Rik\tchr1\t175156866\t175201240\t+\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000070048_ENSMUSG00000056128\tchr1\t92571736\t92576368\t+\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000070987_EG433384\tchr1\t183781705\t183783320\t-\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000072395_Olfr1406\tchr1\t175113651\t175120746\t-\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000094288_Wdr64\tchr1\t177654798\t177798070\t+\t---\t---\t---\t---\t---\t---\t---\n+ENSMUST00000094950_Pgap1\tchr1\t54529849\t54614539\t-\tchr1\t54631692\t54631815\t17153\t17153\tD\tNO\n+ENSMUST00000097776_Cnnm3\tchr1\t36567938\t36585164\t+\t---\t---\t---\t---\t---\t---\t---\n+EU429481_Igfn1\tchr1\t137825893\t137890307\t-\t---\t---\t---\t---\t---\t---\t---\n+FJ024495_Ildr2\tchr1\t168236882\t168239692\t-\t---\t---\t---\t-'..b'6016\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_178779_Rnf152\tchr1\t107176426\t107253513\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_178874_Tmcc2\tchr1\t134252895\t134288369\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_178883_Gorab\tchr1\t165315039\t165340946\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_178884_Obsl1\tchr1\t75482401\t75503218\t-\tchr1\t75481920\t75482054\t347\t21164\tU\tNO\n+NM_181405_Rnpepl1\tchr1\t94807467\t94817954\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_181546_Syt14\tchr1\t194713536\t194861959\t-\tchr1\t194957396\t194957723\t95437\t95437\tD\tNO\n+NM_181750_R3hdm1\tchr1\t129999892\t130134312\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_181796_Gstp2\tchr1\t193897651\t193905509\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_182716_Nfasc\tchr1\t134445291\t134638354\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_182930_Plekha6\tchr1\t135077806\t135200008\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_183019_Arhgef4\tchr1\t34788954\t34873560\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_183022_Accn4\tchr1\t75447063\t75470207\t+\tchr1\t75481920\t75482054\t11713\t34857\tU\tNO\n+NM_183027_Ap1s3\tchr1\t79591820\t79668545\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_183028_Pcmtd1\tchr1\t7079053\t7163709\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_183124_Defb41\tchr1\t18241071\t18350659\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_183355_Pbx1\tchr1\t170049495\t170512777\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_183391_Tnfsf18\tchr1\t163373523\t163524094\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_194333_Slc23a3\tchr1\t75120731\t75130464\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_198006_6330578E17Rik\tchr1\t37473934\t37474944\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_198006_6330578E17Rik\tchr1\t37477057\t37486928\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_198028_Serpinb10\tchr1\t109425580\t109445838\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_198127_Abi2\tchr1\t60466022\t60537998\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_198247_Sertad4\tchr1\t194670313\t194693726\t-\tchr1\t194645118\t194645475\t24838\t48251\tU\tNO\n+NM_198303_Eif5b\tchr1\t38054627\t38112414\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_198652_6430706D22Rik\tchr1\t90158880\t90174174\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_198653_Iars2\tchr1\t187109458\t187153280\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_198654_Nsl1\tchr1\t192886918\t192919389\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_198680_Serpinb3b\tchr1\t109033488\t109059720\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_198899_Ugcgl1\tchr1\t36196873\t36301555\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_198934_Pou2f1\tchr1\t167804181\t167932753\t-\tchr1\t167906284\t167906554\t0\t26199\t.\tYES\n+NM_199007_Sgol2\tchr1\t58026657\t58085164\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_199021_Dpp10\tchr1\t125044486\t126749525\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_201363_Serpinb3c\tchr1\t109088051\t109198931\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_201376_Serpinb3d\tchr1\t108974770\t108980057\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_201641_Ugt1a10\tchr1\t89922380\t90115570\t+\tchr1\t89989553\t89989714\t0\t67173\t.\tYES\n+NM_206896_Olfr12\tchr1\t94516341\t94538591\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_207031_Ano7\tchr1\t95270385\t95302271\t+\tchr1\t95186508\t95186637\t83748\t83748\tD\tNO\n+NM_207137_Olfr417\tchr1\t176299050\t176299979\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_207137_Olfr417\tchr1\t176321202\t176322113\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_207158_Olfr427\tchr1\t176028781\t176030538\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_207225_Hdac4\tchr1\t93755950\t94103099\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_207228_Tsga10\tchr1\t37783457\t37922148\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_207233_C1ql2\tchr1\t122196386\t122239751\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_207281_4832428D23Rik\tchr1\t44260915\t44515719\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_207583_Fam5b\tchr1\t160175402\t160286644\t-\t---\t---\t---\t---\t---\t---\t---\n+NM_207653_Cflar\tchr1\t58768296\t58813658\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_207653_Cflar\tchr1\t58813703\t58815725\t+\t---\t---\t---\t---\t---\t---\t---\n+NM_213616_Atp2b4\tchr1\t135602265\t135697538\t-\tchr1\t135582677\t135582828\t19437\t114710\tU\tNO\n+NR_002840_Gas5\tchr1\t162964758\t162968663\t+\t---\t---\t---\t---\t---\t---\t---\n+NR_002858_EG241041\tchr1\t21268965\t21306401\t-\t---\t---\t---\t---\t---\t---\t---\n+NR_002870_Dnm3os\tchr1\t164119785\t164155671\t+\tchr1\t164215623\t164215935\t59952\t95838\tU\tNO\n+NR_003623_EG277333\tchr1\t182251970\t182262902\t-\t---\t---\t---\t---\t---\t---\t---\n+NR_026896_4931440L10Rik\tchr1\t136437533\t136449760\t-\t---\t---\t---\t---\t---\t---\t---\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/peaks_per_feature3.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks_per_feature3.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| @@ -0,0 +1,30 @@ +#gene.id gene.chr gene.start gene.end gene.strand chr_1 start_1 end_1 dist_closest_1 dist_TSS_1 direction_1 in_the_gene_1 chr_2 start_2 end_2 dist_closest_2 dist_TSS_2 direction_2 in_the_gene_2 chr_3 start_3 end_3 dist_closest_3 dist_TSS_3 direction_3 in_the_gene_3 chr_4 start_4 end_4 dist_closest_4 dist_TSS_4 direction_4 in_the_gene_4 +AF064749_Col6a3 chr1 92566771 92800755 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +AK015559_4930472D16Rik chr1 25020851 25021989 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +AK030377_A330023F24Rik chr1 196781953 196826186 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +AK080193_A530079E22Rik chr1 89401837 89403491 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +AK082264_C230030N03Rik chr1 34735043 34781084 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC006931_AI597479 chr1 43153807 43172843 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC021773_Glb1l chr1 75193364 75207353 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC023951_D1Ertd622e chr1 99540054 99558631 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC028767_3110009E18Rik chr1 122017764 122114603 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC031781_BC031781 chr1 182781250 182798240 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC034187_BC035947 chr1 78493611 78497758 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC043098_Fam168b chr1 34870072 34917183 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC049091_D1Bwg0212e chr1 39592545 39603734 + chr1 39492140 39492513 100032 100032 D NO . . . . . . . . . . . . . . . . . . . . . +BC049713_Ankrd45 chr1 163072817 163099826 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC050813_4921511C04Rik chr1 37157481 37244861 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC051128_4921521F21Rik chr1 65059273 65079312 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC052693_2810422O20Rik chr1 165924541 165927371 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC052931_A630001G21Rik chr1 87601462 87674840 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC053100_5730559C18Rik chr1 138110108 138130841 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC054802_9630058J23Rik chr1 181476521 181558044 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC055845_2810025M15Rik chr1 159342483 159350353 + chr1 159240736 159240866 101617 101617 D NO . . . . . . . . . . . . . . . . . . . . . +BC055955_A130010J15Rik chr1 194999663 195004015 + chr1 194957396 194957723 41940 41940 D NO . . . . . . . . . . . . . . . . . . . . . +BC057872_Rab3gap2 chr1 187028006 187110623 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC058417_2610017I09Rik chr1 42648822 42751667 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC059254_Phlpp chr1 108042052 108306367 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC070435_Fam123c chr1 34620070 34671545 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC070446_Fam135a chr1 24017617 24107170 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC071241_9430016H08Rik chr1 57463192 57497936 + . . . . . . . . . . . . . . . . . . . . . . . . . . . . +BC072639_2010300C02Rik chr1 37646877 37776659 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/peaks_per_feature4.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks_per_feature4.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,3825 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| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/peaks_per_feature4.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaks_per_feature4.summary Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,957 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|
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/peaks_to_transcripts.out --- a/test-data/peaks_to_transcripts.out Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,957 +0,0 @@\n-#geneID\tchr_RNA\tstart\tend\tstrand\tdifferentially_expressed\tnumber_of_peaks\n-AF064749_Col6a3\tchr1\t92566771\t92800755\t-\t1\t0\n-AK015559_4930472D16Rik\tchr1\t25020851\t25021989\t-\t1\t0\n-AK030377_A330023F24Rik\tchr1\t196781953\t196826186\t-\t1\t0\n-AK080193_A530079E22Rik\tchr1\t89401837\t89403491\t-\t1\t0\n-AK082264_C230030N03Rik\tchr1\t34735043\t34781084\t+\t1\t0\n-BC006931_AI597479\tchr1\t43153807\t43172843\t+\t1\t0\n-BC021773_Glb1l\tchr1\t75193364\t75207353\t-\t1\t0\n-BC023951_D1Ertd622e\tchr1\t99540054\t99558631\t-\t1\t0\n-BC028767_3110009E18Rik\tchr1\t122017764\t122114603\t+\t1\t0\n-BC031781_BC031781\tchr1\t182781250\t182798240\t+\t1\t0\n-BC034187_BC035947\tchr1\t78493611\t78497758\t-\t1\t0\n-BC043098_Fam168b\tchr1\t34870072\t34917183\t-\t1\t0\n-BC049091_D1Bwg0212e\tchr1\t39592545\t39603734\t+\t1\t0\n-BC049713_Ankrd45\tchr1\t163072817\t163099826\t+\t1\t0\n-BC050813_4921511C04Rik\tchr1\t37157481\t37244861\t+\t1\t0\n-BC051128_4921521F21Rik\tchr1\t65059273\t65079312\t-\t1\t0\n-BC052693_2810422O20Rik\tchr1\t165924541\t165927371\t+\t1\t0\n-BC052931_A630001G21Rik\tchr1\t87601462\t87674840\t-\t1\t0\n-BC053100_5730559C18Rik\tchr1\t138110108\t138130841\t-\t1\t0\n-BC054802_9630058J23Rik\tchr1\t181476521\t181558044\t+\t1\t0\n-BC055845_2810025M15Rik\tchr1\t159342483\t159350353\t+\t1\t0\n-BC055955_A130010J15Rik\tchr1\t194999663\t195004015\t+\t1\t0\n-BC057872_Rab3gap2\tchr1\t187028006\t187110623\t+\t1\t0\n-BC058417_2610017I09Rik\tchr1\t42648822\t42751667\t-\t1\t0\n-BC059254_Phlpp\tchr1\t108042052\t108306367\t+\t1\t0\n-BC070435_Fam123c\tchr1\t34620070\t34671545\t+\t1\t0\n-BC070446_Fam135a\tchr1\t24017617\t24107170\t-\t1\t0\n-BC071241_9430016H08Rik\tchr1\t57463192\t57497936\t+\t1\t0\n-BC072639_2010300C02Rik\tchr1\t37646877\t37776659\t-\t1\t0\n-BC080290_5033414K04Rik\tchr1\t84032539\t84360735\t-\t0\t0\n-BC082310_9430031J16Rik\tchr1\t81073525\t81338329\t+\t0\t0\n-BC089525_2310007B03Rik\tchr1\t95047933\t95063386\t-\t0\t0\n-BC089561_Cep350\tchr1\t157692096\t157820375\t-\t0\t0\n-BC147491_A230074B11Rik\tchr1\t37083441\t37133840\t+\t0\t0\n-BC147657_9630028B13Rik\tchr1\t187253234\t187265698\t-\t0\t0\n-ENSMUST00000027997_Rgs5\tchr1\t171625108\t171625913\t+\t0\t0\n-ENSMUST00000051203_1700001G17Rik\tchr1\t33726669\t33727551\t+\t0\t0\n-ENSMUST00000054333_A130050O07Rik\tchr1\t139823828\t139826840\t+\t0\t0\n-ENSMUST00000056879_C230029F24Rik\tchr1\t49301475\t49397265\t+\t0\t0\n-ENSMUST00000057543_A730013G03Rik\tchr1\t194659323\t194661397\t-\t0\t0\n-ENSMUST00000062637_4930470H14Rik\tchr1\t175156866\t175201240\t+\t0\t0\n-ENSMUST00000070048_ENSMUSG00000056128\tchr1\t92571736\t92576368\t+\t0\t0\n-ENSMUST00000070987_EG433384\tchr1\t183781705\t183783320\t-\t0\t0\n-ENSMUST00000072395_Olfr1406\tchr1\t175113651\t175120746\t-\t0\t0\n-ENSMUST00000094288_Wdr64\tchr1\t177654798\t177798070\t+\t0\t0\n-ENSMUST00000094950_Pgap1\tchr1\t54529849\t54614539\t-\t0\t0\n-ENSMUST00000097776_Cnnm3\tchr1\t36567938\t36585164\t+\t0\t0\n-EU429481_Igfn1\tchr1\t137825893\t137890307\t-\t0\t0\n-FJ024495_Ildr2\tchr1\t168236882\t168239692\t-\t0\t0\n-FJ210934_Unc80\tchr1\t66514856\t66556109\t+\t0\t0\n-NM_001001565_Chpf\tchr1\t75470923\t75476437\t-\t0\t0\n-NM_001001809_Olfr218\tchr1\t175130421\t175134469\t+\t0\t0\n-NM_001001883_Hecw2\tchr1\t53867026\t54252002\t-\t0\t0\n-NM_001003917_Atg9a\tchr1\t75177439\t75189181\t-\t0\t0\n-NM_001004173_Sgpp2\tchr1\t78306692\t78416864\t+\t0\t0\n-NM_001005423_Mreg\tchr1\t72170192\t72258895\t-\t0\t0\n-NM_001005507_Smg7\tchr1\t154684125\t154750410\t-\t0\t0\n-NM_001005508_Arhgap30\tchr1\t173319072\t173340822\t+\t0\t0\n-NM_001005520_Olfr244\tchr1\t176032571\t176067605\t-\t0\t0\n-NM_001008419_Aox3l1\tchr1\t58335180\t58437083\t+\t0\t0\n-NM_001008426_EG433365\tchr1\t155721475\t155724001\t+\t0\t0\n-NM_001008533_Adora1\tchr1\t136095799\t136181661\t-\t0\t0\n-NM_001009940_Il19\tchr1\t132786042\t132915234\t-\t0\t0\n-NM_001011525_Olfr1415\tchr1\t94376258\t94381054\t-\t0\t0\n-NM_001011525_Olfr1415\tchr1\t94407669\t94418761\t-\t0\t0\n-NM_001011684_Nms\tchr1\t38995917\t39007113\t+\t0\t0\n-NM_001011873_Xkr9\tchr1\t13658862\t13691794\t+\t0\t0\n-NM_001011874_Xkr4\tchr1\t3203722\t3713108\t-\t0\t0\n-NM_001012330_Zfp238\tchr1\t179359958\t179380892\t+\t0\t0\n-NM_001013374_Lman2l\tchr1\t36362897\t36502078\t-\t0\t0\n-NM_001013382_Lrrc52\tchr1\t169375806\t169397136\t-\t0\t0\n-NM_001013771_Gm973\tchr1\t59573136\t59693241\t+\t0\t0\n-NM_001013779_Aim2\tchr1\t175385835\t175396165\t+\t0\t0\n-NM_001014974_Ttll4\tchr1\t74708314\t74748400\t+\t0\t0\n-NM_001024721_BC094916\tchr1\t'..b'77604_AA986860\tchr1\t132628563\t132644539\t+\t0\t0\n-NM_177643_Zfp281\tchr1\t138487073\t138526617\t+\t0\t0\n-NM_177646_Dgkd\tchr1\t89749836\t89841946\t+\t0\t0\n-NM_177722_6030422M02Rik\tchr1\t9898713\t9932156\t+\t0\t0\n-NM_177723_Vsig8\tchr1\t174486069\t174513273\t+\t0\t0\n-NM_177724_D230039L06Rik\tchr1\t180426979\t180686112\t+\t0\t0\n-NM_177756_Glt25d2\tchr1\t154223175\t154357825\t+\t0\t0\n-NM_177757_Kif26b\tchr1\t180720593\t180862983\t+\t0\t0\n-NM_177781_Trpa1\tchr1\t14861962\t14909072\t-\t0\t0\n-NM_177834_Cpa6\tchr1\t10314801\t10710026\t-\t0\t0\n-NM_177838_Fam163a\tchr1\t157923096\t158135544\t-\t0\t0\n-NM_177839_Tnn\tchr1\t161966935\t162084477\t-\t0\t0\n-NM_178051_Mterfd2\tchr1\t95195779\t95202630\t-\t0\t0\n-NM_178055_Dnajb2\tchr1\t75233016\t75242264\t+\t0\t0\n-NM_178119_Agap1\tchr1\t91351421\t91791845\t+\t0\t0\n-NM_178241_Il8ra\tchr1\t74238380\t74241205\t-\t0\t0\n-NM_178243_5830403L16Rik\tchr1\t155697272\t155747352\t-\t0\t0\n-NM_178244_Teddm1\tchr1\t155724147\t155740188\t+\t0\t0\n-NM_178399_3110035E14Rik\tchr1\t9591248\t9617222\t+\t0\t0\n-NM_178405_Atp1a2\tchr1\t174201852\t174233438\t-\t0\t0\n-NM_178593_Rcsd1\tchr1\t167572007\t167639868\t-\t0\t0\n-NM_178598_Tagln2\tchr1\t174430123\t174475991\t+\t0\t0\n-NM_178601_Imp4\tchr1\t34496377\t34511555\t+\t0\t0\n-NM_178632_Ints7\tchr1\t193399085\t193447550\t+\t0\t0\n-NM_178653_Sccpdh\tchr1\t181598088\t181617593\t+\t0\t0\n-NM_178690_Rab3gap1\tchr1\t129765355\t129840723\t+\t0\t0\n-NM_178691_Yod1\tchr1\t132612680\t132618643\t+\t0\t0\n-NM_178692_C130074G19Rik\tchr1\t186695805\t186707077\t-\t0\t0\n-NM_178775_Rps6kc1\tchr1\t192524091\t192736016\t-\t0\t0\n-NM_178779_Rnf152\tchr1\t107176426\t107253513\t-\t0\t0\n-NM_178874_Tmcc2\tchr1\t134252895\t134288369\t-\t0\t0\n-NM_178883_Gorab\tchr1\t165315039\t165340946\t-\t0\t0\n-NM_178884_Obsl1\tchr1\t75482401\t75503218\t-\t0\t0\n-NM_181405_Rnpepl1\tchr1\t94807467\t94817954\t+\t0\t0\n-NM_181546_Syt14\tchr1\t194713536\t194861959\t-\t0\t0\n-NM_181750_R3hdm1\tchr1\t129999892\t130134312\t+\t0\t0\n-NM_181796_Gstp2\tchr1\t193897651\t193905509\t-\t0\t0\n-NM_182716_Nfasc\tchr1\t134445291\t134638354\t-\t0\t0\n-NM_182930_Plekha6\tchr1\t135077806\t135200008\t+\t0\t0\n-NM_183019_Arhgef4\tchr1\t34788954\t34873560\t+\t0\t0\n-NM_183022_Accn4\tchr1\t75447063\t75470207\t+\t0\t0\n-NM_183027_Ap1s3\tchr1\t79591820\t79668545\t-\t0\t0\n-NM_183028_Pcmtd1\tchr1\t7079053\t7163709\t+\t0\t0\n-NM_183124_Defb41\tchr1\t18241071\t18350659\t-\t0\t0\n-NM_183355_Pbx1\tchr1\t170049495\t170512777\t-\t0\t0\n-NM_183391_Tnfsf18\tchr1\t163373523\t163524094\t+\t0\t0\n-NM_194333_Slc23a3\tchr1\t75120731\t75130464\t-\t0\t0\n-NM_198006_6330578E17Rik\tchr1\t37473934\t37474944\t-\t0\t0\n-NM_198006_6330578E17Rik\tchr1\t37477057\t37486928\t-\t0\t0\n-NM_198028_Serpinb10\tchr1\t109425580\t109445838\t+\t0\t0\n-NM_198127_Abi2\tchr1\t60466022\t60537998\t+\t0\t0\n-NM_198247_Sertad4\tchr1\t194670313\t194693726\t-\t0\t0\n-NM_198303_Eif5b\tchr1\t38054627\t38112414\t+\t0\t0\n-NM_198652_6430706D22Rik\tchr1\t90158880\t90174174\t-\t0\t0\n-NM_198653_Iars2\tchr1\t187109458\t187153280\t-\t0\t0\n-NM_198654_Nsl1\tchr1\t192886918\t192919389\t+\t0\t0\n-NM_198680_Serpinb3b\tchr1\t109033488\t109059720\t-\t0\t0\n-NM_198899_Ugcgl1\tchr1\t36196873\t36301555\t-\t0\t0\n-NM_198934_Pou2f1\tchr1\t167804181\t167932753\t-\t0\t0\n-NM_199007_Sgol2\tchr1\t58026657\t58085164\t+\t0\t0\n-NM_199021_Dpp10\tchr1\t125044486\t126749525\t-\t0\t0\n-NM_201363_Serpinb3c\tchr1\t109088051\t109198931\t-\t0\t0\n-NM_201376_Serpinb3d\tchr1\t108974770\t108980057\t-\t0\t0\n-NM_201641_Ugt1a10\tchr1\t89922380\t90115570\t+\t0\t0\n-NM_206896_Olfr12\tchr1\t94516341\t94538591\t+\t0\t0\n-NM_207031_Ano7\tchr1\t95270385\t95302271\t+\t0\t0\n-NM_207137_Olfr417\tchr1\t176299050\t176299979\t+\t0\t0\n-NM_207137_Olfr417\tchr1\t176321202\t176322113\t+\t0\t0\n-NM_207158_Olfr427\tchr1\t176028781\t176030538\t+\t0\t0\n-NM_207225_Hdac4\tchr1\t93755950\t94103099\t-\t0\t0\n-NM_207228_Tsga10\tchr1\t37783457\t37922148\t-\t0\t0\n-NM_207233_C1ql2\tchr1\t122196386\t122239751\t+\t0\t0\n-NM_207281_4832428D23Rik\tchr1\t44260915\t44515719\t-\t0\t0\n-NM_207583_Fam5b\tchr1\t160175402\t160286644\t-\t0\t0\n-NM_207653_Cflar\tchr1\t58768296\t58813658\t+\t0\t0\n-NM_207653_Cflar\tchr1\t58813703\t58815725\t+\t0\t0\n-NM_213616_Atp2b4\tchr1\t135602265\t135697538\t-\t0\t0\n-NR_002840_Gas5\tchr1\t162964758\t162968663\t+\t0\t0\n-NR_002858_EG241041\tchr1\t21268965\t21306401\t-\t0\t0\n-NR_002870_Dnm3os\tchr1\t164119785\t164155671\t+\t0\t0\n-NR_003623_EG277333\tchr1\t182251970\t182262902\t-\t0\t0\n-NR_026896_4931440L10Rik\tchr1\t136437533\t136449760\t-\t0\t0\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/summits.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summits.txt Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,654 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\n+chr6\t128326644\t128326645\r\n+chr6\t128547343\t128547344\r\n+chr6\t134445175\t134445176\r\n+chr6\t134445312\t134445313\r\n+chr6\t143811364\t143811365\r\n+chr6\t146887669\t146887670\r\n+chr6\t147297840\t147297841\r\n+chr6\t17267124\t17267125\r\n+chr6\t33926636\t33926637\r\n+chr6\t37242315\t37242316\r\n+chr6\t47601314\t47601315\r\n+chr6\t49172166\t49172167\r\n+chr6\t51351355\t51351356\r\n+chr6\t56806957\t56806958\r\n+chr6\t67253361\t67253362\r\n+chr6\t76927942\t76927943\r\n+chr6\t83071812\t83071813\r\n+chr6\t83093011\t83093012\r\n+chr6\t86130730\t86130731\r\n+chr6\t87137073\t87137074\r\n+chr6\t87222111\t87222112\r\n+chr6\t94625281\t94625282\r\n+chr7\t104849801\t104849802\r\n+chr7\t117975070\t117975071\r\n+chr7\t119647132\t119647133\r\n+chr7\t119813749\t119813750\r\n+chr7\t120393123\t120393124\r\n+chr7\t120874367\t120874368\r\n+chr7\t123336714\t123336715\r\n+chr7\t125720143\t125720144\r\n+chr7\t126039427\t126039428\r\n+chr7\t127004913\t127004914\r\n+chr7\t128854935\t128854936\r\n+chr7\t128984541\t128984542\r\n+chr7\t134819118\t134819119\r\n+chr7\t135696903\t135696904\r\n+chr7\t137484210\t137484211\r\n+chr7\t137768001\t137768002\r\n+chr7\t138009297\t138009298\r\n+chr7\t138123566\t138123567\r\n+chr7\t138123699\t138123700\r\n+chr7\t139426142\t139426143\r\n+chr7\t146041529\t146041530\r\n+chr7\t147156352\t147156353\r\n+chr7\t148379180\t148379181\r\n+chr7\t148379362\t148379363\r\n+chr7\t148629281\t148629282\r\n+chr7\t150571560\t150571561\r\n+chr7\t152450338\t152450339\r\n+chr7\t152450519\t152450520\r\n+chr7\t16562058\t16562059\r\n+chr7\t16894872\t16894873\r\n+chr7\t17429367\t17429368\r\n+chr7\t20044401\t20044402\r\n+chr7\t26061110\t26061111\r\n+chr7\t26574315\t26574316\r\n+chr7\t28010205\t28010206\r\n+chr7\t30227710\t30227711\r\n+chr7\t30256558\t30256559\r\n+chr7\t35861923\t35861924\r\n+chr7\t56809068\t56809069\r\n+chr7\t87336398\t87336399\r\n+chr7\t88092779\t88092780\r\n+chr7\t89920499\t89920500\r\n+chr8\t10576464\t10576465\r\n+chr8\t107426996\t107426997\r\n+chr8\t109087961\t109087962\r\n+chr8\t109275046\t109275047\r\n+chr8\t109334564\t109334565\r\n+chr8\t113806188\t113806189\r\n+chr8\t119851483\t119851484\r\n+chr8\t121354388\t121354389\r\n+chr8\t129127362\t129127363\r\n+chr8\t129549456\t129549457\r\n+chr8\t13548998\t13548999\r\n+chr8\t13668465\t13668466\r\n+chr8\t14306960\t14306961\r\n+chr8\t17594804\t17594805\r\n+chr8\t19919526\t19919527\r\n+chr8\t19924810\t19924811\r\n+chr8\t22870138\t22870139\r\n+chr8\t23921280\t23921281\r\n+chr8\t24206095\t24206096\r\n+chr8\t34068894\t34068895\r\n+chr8\t37107644\t37107645\r\n+chr8\t4586605\t4586606\r\n+chr8\t70850825\t70850826\r\n+chr8\t71717281\t71717282\r\n+chr8\t73173598\t73173599\r\n+chr8\t73183558\t73183559\r\n+chr8\t73297497\t73297498\r\n+chr8\t81256455\t81256456\r\n+chr8\t86143616\t86143617\r\n+chr8\t87180694\t87180695\r\n+chr8\t88126748\t88126749\r\n+chr8\t93828640\t93828641\r\n+chr8\t97699878\t97699879\r\n+chr9\t100543647\t100543648\r\n+chr9\t103988283\t103988284\r\n+chr9\t106273656\t106273657\r\n+chr9\t107478162\t107478163\r\n+chr9\t108851463\t108851464\r\n+chr9\t110183808\t110183809\r\n+chr9\t111053664\t111053665\r\n+chr9\t116828689\t116828690\r\n+chr9\t118884586\t118884587\r\n+chr9\t120883928\t120883929\r\n+chr9\t123371104\t123371105\r\n+chr9\t13408238\t13408239\r\n+chr9\t14466849\t14466850\r\n+chr9\t14480293\t14480294\r\n+chr9\t24346538\t24346539\r\n+chr9\t3258857\t3258858\r\n+chr9\t42777363\t42777364\r\n+chr9\t43528251\t43528252\r\n+chr9\t43585984\t43585985\r\n+chr9\t44215148\t44215149\r\n+chr9\t44307103\t44307104\r\n+chr9\t54460731\t54460732\r\n+chr9\t66728918\t66728919\r\n+chr9\t66794084\t66794085\r\n+chr9\t67556540\t67556541\r\n+chr9\t70477636\t70477637\r\n+chr9\t72497695\t72497696\r\n+chr9\t72916030\t72916031\r\n+chr9\t74815214\t74815215\r\n+chr9\t75371664\t75371665\r\n+chr9\t8033087\t8033088\r\n+chr9\t8055015\t8055016\r\n+chr9\t83462792\t83462793\r\n+chr9\t86714892\t86714893\r\n+chrX\t109484691\t109484692\r\n+chrX\t137172820\t137172821\r\n+chrX\t139917606\t139917607\r\n+chrX\t140401017\t140401018\r\n+chrX\t163589625\t163589626\r\n+chrX\t166360754\t166360755\r\n+chrX\t166427362\t166427363\r\n+chrX\t166432950\t166432951\r\n+chrX\t84483714\t84483715\r\n+chrX\t98516735\t98516736\r\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/summits.xls |
| b |
| Binary file test-data/summits.xls has changed |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/summits.xlsx |
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| Binary file test-data/summits.xlsx has changed |
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| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/summits_per_feature.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summits_per_feature.out Wed Feb 24 09:39:14 2016 -0500 |
| b |
| b'@@ -0,0 +1,957 @@\n+#gene.id\tgene.chr\tgene.start\tgene.end\tgene.strand\tchr_1\tstart_1\tend_1\tdist_closest_1\tdist_TSS_1\tdirection_1\tin_the_gene_1\tchr_2\tstart_2\tend_2\tdist_closest_2\tdist_TSS_2\tdirection_2\tin_the_gene_2\tchr_3\tstart_3\tend_3\tdist_closest_3\tdist_TSS_3\tdirection_3\tin_the_gene_3\tchr_4\tstart_4\tend_4\tdist_closest_4\tdist_TSS_4\tdirection_4\tin_the_gene_4\n+AF064749_Col6a3\tchr1\t92566771\t92800755\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+AK015559_4930472D16Rik\tchr1\t25020851\t25021989\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+AK030377_A330023F24Rik\tchr1\t196781953\t196826186\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+AK080193_A530079E22Rik\tchr1\t89401837\t89403491\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+AK082264_C230030N03Rik\tchr1\t34735043\t34781084\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC006931_AI597479\tchr1\t43153807\t43172843\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC021773_Glb1l\tchr1\t75193364\t75207353\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC023951_D1Ertd622e\tchr1\t99540054\t99558631\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC028767_3110009E18Rik\tchr1\t122017764\t122114603\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC031781_BC031781\tchr1\t182781250\t182798240\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC034187_BC035947\tchr1\t78493611\t78497758\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC043098_Fam168b\tchr1\t34870072\t34917183\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC049091_D1Bwg0212e\tchr1\t39592545\t39603734\t+\tchr1\t39502327\t39502328\t90217\t90217\tD\tNO\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC049713_Ankrd45\tchr1\t163072817\t163099826\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC050813_4921511C04Rik\tchr1\t37157481\t37244861\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC051128_4921521F21Rik\tchr1\t65059273\t65079312\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC052693_2810422O20Rik\tchr1\t165924541\t165927371\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC052931_A630001G21Rik\tchr1\t87601462\t87674840\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC053100_5730559C18Rik\tchr1\t138110108\t138130841\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC054802_9630058J23Rik\tchr1\t181476521\t181558044\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC055845_2810025M15Rik\tchr1\t159342483\t159350353\t+\tchr1\t159250801\t159250802\t91681\t91681\tD\tNO\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC055955_A130010J15Rik\tchr1\t194999663\t195004015\t+\tchr1\t194967560\t194967561\t32102\t32102\tD\tNO\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC057872_Rab3gap2\tchr1\t187028006\t187110623\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC058417_2610017I09Rik\tchr1\t42648822\t42751667\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC059254_Phlpp\tchr1\t108042052\t108306367\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC070435_Fam123c\tchr1\t34620070\t34671545\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC070446_Fam135a\tchr1\t24017617\t24107170\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC071241_9430016H08Rik\tchr1\t57463192\t57497936\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC072639_2010300C02Rik\tchr1\t37646877\t37776659\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC080290_5033414K04Rik\tchr1\t84032539\t84360735\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC082310_9430031J16Rik\tchr1\t81073525\t81338329\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC089525_2310007B03Rik\tchr1\t95047933\t95063386\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC089561_Cep350\tchr1\t157692096\t157820375\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC147491_A230074B11Rik\tchr1\t37083441\t37133840\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+BC147657_9630028B13Rik\tchr1\t187253234\t1872656'..b'_183355_Pbx1\tchr1\t170049495\t170512777\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_183391_Tnfsf18\tchr1\t163373523\t163524094\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_194333_Slc23a3\tchr1\t75120731\t75130464\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198006_6330578E17Rik\tchr1\t37473934\t37474944\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198006_6330578E17Rik\tchr1\t37477057\t37486928\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198028_Serpinb10\tchr1\t109425580\t109445838\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198127_Abi2\tchr1\t60466022\t60537998\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198247_Sertad4\tchr1\t194670313\t194693726\t-\tchr1\t194655297\t194655298\t15015\t38428\tU\tNO\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198303_Eif5b\tchr1\t38054627\t38112414\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198652_6430706D22Rik\tchr1\t90158880\t90174174\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198653_Iars2\tchr1\t187109458\t187153280\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198654_Nsl1\tchr1\t192886918\t192919389\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198680_Serpinb3b\tchr1\t109033488\t109059720\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198899_Ugcgl1\tchr1\t36196873\t36301555\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_198934_Pou2f1\tchr1\t167804181\t167932753\t-\tchr1\t167916419\t167916420\t0\t16333\t.\tYES\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_199007_Sgol2\tchr1\t58026657\t58085164\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_199021_Dpp10\tchr1\t125044486\t126749525\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_201363_Serpinb3c\tchr1\t109088051\t109198931\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_201376_Serpinb3d\tchr1\t108974770\t108980057\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_201641_Ugt1a10\tchr1\t89922380\t90115570\t+\tchr1\t89999634\t89999635\t0\t77254\t.\tYES\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_206896_Olfr12\tchr1\t94516341\t94538591\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207031_Ano7\tchr1\t95270385\t95302271\t+\tchr1\t95196573\t95196574\t73811\t73811\tD\tNO\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207137_Olfr417\tchr1\t176299050\t176299979\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207137_Olfr417\tchr1\t176321202\t176322113\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207158_Olfr427\tchr1\t176028781\t176030538\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207225_Hdac4\tchr1\t93755950\t94103099\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207228_Tsga10\tchr1\t37783457\t37922148\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207233_C1ql2\tchr1\t122196386\t122239751\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207281_4832428D23Rik\tchr1\t44260915\t44515719\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207583_Fam5b\tchr1\t160175402\t160286644\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207653_Cflar\tchr1\t58768296\t58813658\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_207653_Cflar\tchr1\t58813703\t58815725\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NM_213616_Atp2b4\tchr1\t135602265\t135697538\t-\tchr1\t135592753\t135592754\t9511\t104784\tU\tNO\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NR_002840_Gas5\tchr1\t162964758\t162968663\t+\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NR_002858_EG241041\tchr1\t21268965\t21306401\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NR_002870_Dnm3os\tchr1\t164119785\t164155671\t+\tchr1\t164225779\t164225780\t70108\t105994\tU\tNO\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NR_003623_EG277333\tchr1\t182251970\t182262902\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n+NR_026896_4931440L10Rik\tchr1\t136437533\t136449760\t-\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/transcripts_to_edges.out --- a/test-data/transcripts_to_edges.out Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -#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 |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/transcripts_to_edges.summary --- a/test-data/transcripts_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -#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 |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/tss_to_edges.out --- a/test-data/tss_to_edges.out Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -#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 |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/tss_to_edges.summary --- a/test-data/tss_to_edges.summary Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -#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 |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 test-data/tss_to_summits.out --- a/test-data/tss_to_summits.out Tue Jun 30 06:44:06 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,654 +0,0 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of 1\t159342483\t91682\t99552\t+\tNO\t0\t\n-chr11\t59272503\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t6069204\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t163837980\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t164225779\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t167233113\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t167916419\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t69572437\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t170265171\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t70397406\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t17040475\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t172630846\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t172630999\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t174386565\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t76126479\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t181071373\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t182489776\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t83860977\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t84381942\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t8483612\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t8541945\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t185865026\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t87257043\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t87967409\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t87967599\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr11\t93986729\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t194268840\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t194655297\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t194967560\tBC055955_A130010J15Rik\t1 of 1\t194999663\t32103\t36455\t+\tNO\t1\tNM_016851_Irf6\n-chr1\t195334592\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t195340816\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t195348466\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr1\t'..b'1\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t104849801\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t117975070\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t119647132\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t119813749\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t120393123\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t120874367\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t123336714\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t125720143\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t126039427\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t127004913\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t128854935\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t128984541\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t134819118\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t135696903\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t137484210\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t137768001\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t138009297\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t138123566\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t138123699\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t139426142\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t146041529\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t147156352\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t148379180\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t148379362\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t148629281\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t150571560\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t152450338\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t152450519\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t16562058\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t16894872\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t17429367\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t20044401\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t26061110\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t26574315\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t28010205\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t30227710\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t30256558\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t35861923\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t56809068\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t87336398\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t88092779\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr7\t89920499\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t10576464\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t107426996\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t109087961\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t109275046\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t109334564\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t113806188\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t119851483\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t121354388\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t129127362\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t129549456\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t13548998\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t13668465\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t14306960\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t17594804\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t19919526\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t19924810\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t22870138\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t23921280\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t24206095\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t34068894\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t37107644\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t4586605\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t70850825\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t71717281\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t73173598\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t73183558\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t73297497\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t81256455\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t86143616\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t87180694\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t88126748\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t93828640\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr8\t97699878\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t100543647\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t103988283\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t106273656\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t107478162\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t108851463\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t110183808\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t111053664\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t116828689\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t118884586\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t120883928\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t123371104\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t13408238\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t14466849\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t14480293\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t24346538\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t3258857\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t42777363\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t43528251\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t43585984\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t44215148\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t44307103\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t54460731\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t66728918\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t66794084\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t67556540\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t70477636\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t72497695\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t72916030\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t74815214\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t75371664\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t8033087\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t8055015\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t83462792\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chr9\t86714892\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t109484691\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t137172820\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t139917606\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t140401017\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t163589625\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t166360754\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t166427362\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t166432950\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t84483714\t.\t.\t.\t.\t.\t.\t.\t.\t.\n-chrX\t98516735\t.\t.\t.\t.\t.\t.\t.\t.\t.\n' |
| b |
| diff -r d9c1f2133124 -r 5f69a2c1b9c9 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 30 06:44:06 2015 -0400 +++ b/tool_dependencies.xml Wed Feb 24 09:39:14 2016 -0500 |
| b |
| @@ -1,26 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="python_xlwt" version="0.7.5"> + <package name="python_xlsxwriter" version="0.8.4"> <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">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>Installs Python module xlwt 0.7.5</readme> - </package> - <package name="python_xlrd" version="0.9.3"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://pypi.python.org/packages/source/x/xlrd/xlrd-0.9.3.tar.gz</action> + <action type="download_by_url">https://pypi.python.org/packages/source/X/XlsxWriter/XlsxWriter-0.8.4.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && @@ -32,43 +15,21 @@ </action> </actions> </install> - <readme>Installs Python module xlrd 0.9.3</readme> + <readme>Installs Python module XlsxWriter 0.8.4</readme> </package> - <package name="python_xlutils" version="1.7.1"> + <package name="rnachipintegrator" version="1.0.0"> <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">$INSTALL_DIR/lib/python</action> + <action type="download_by_url">https://pypi.python.org/packages/source/R/RnaChipIntegrator/RnaChipIntegrator-1.0.0.tar.gz</action> <action type="shell_command"> - export PYTHONPATH=$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>$INSTALL_DIR</destination> + pip install --no-use-wheel --install-option "--prefix=$INSTALL_DIR" . </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> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable> </action> </actions> </install> - <readme>Installs RnaChipIntegrator 0.4.3</readme> + <readme>Installs RnaChipIntegrator 1.0.0 from PyPI</readme> </package> </tool_dependency> |