changeset 0:f411ce97a351 draft

Uploaded initial version 1.0.2-2
author pjbriggs
date Tue, 30 Jun 2015 07:08:05 -0400
parents
children df9033b88b53
files README.rst ceas_wrapper.sh ceas_wrapper.xml data_manager/data_manager_ceas_fetch_annotations.py data_manager/data_manager_ceas_fetch_annotations.xml data_manager_conf.xml test-data/ceas.loc test-data/ceas_in.bed test-data/ceas_in.bigwig test-data/ceas_in.wig test-data/ceas_out1.log test-data/ceas_out1.log.re_match test-data/ceas_out1.pdf test-data/ceas_out1.xls test-data/ceas_out2.log test-data/ceas_out2.log.re_match test-data/ceas_out2.pdf test-data/ceas_out2.xls test-data/ceas_out3.log test-data/ceas_out3.log.re_match test-data/ceas_out3.pdf test-data/ceas_out3.xls test-data/galGal3.len test-data/galGal3.refGene tool-data/ceas.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test tool_dependencies.xml
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,84 @@
+CEAS: Cis-regulatory Element Annotation System
+==============================================
+
+Galaxy tool wrapper for the CEAS (Cis-regulatory Element Annotation System), which
+can be used to annotate intervals and scores with genome features.
+
+This tool uses the Cistrome version of the package, which provides two versions of
+the core program: in addition to the ``ceas`` program (the same as that available
+from the main CEAS website), it also includes the ``ceasBW`` program (which can handle
+bigwig input).
+
+The tool assumes that the ``ceas`` and ``ceasBW`` programs are on the Galaxy user's
+path.
+
+The official CEAS website is at:
+
+- http://liulab.dfci.harvard.edu/CEAS/index.html
+
+The Cistrome version can be found via
+
+- https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
+
+Automated installation
+======================
+
+Installation via the Galaxy Tool Shed will take care of installing the tool wrapper
+and the CEAS programs, and setting the appropriate environment variables.
+
+In addition this will also install a data manager which can be used to install
+reference GDB data files necessary for the tool.
+
+Manual Installation
+===================
+
+There are two files to install:
+
+- ``ceas_wrapper.xml`` (the Galaxy tool definition)
+- ``ceas_wrapper.sh`` (the shell script wrapper)
+
+The suggested location is in a ``tools/ceas/`` folder. You will then
+need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
+by adding the line:
+
+    <tool file="ceas/ceasbw_wrapper.xml" />
+
+You also need to make a copy of the ``ceas.loc`` file (a sample version is
+provided here) which points to the available GDB files for different genomes.
+
+This file should be placed in the ``tool-data`` directory of your Galaxy
+installation.
+
+Reference Data
+==============
+
+CEAS requires reference data in the form of GDB files (essentially, SQLite database
+files) containing the RefSeq genes for the genome in question.
+
+A limited number of GDB files are available for download from the CEAS website; to
+make new ones, see the section "Build a sqlite3 file with a gene annotation table
+and genome background annotation for CEAS" in the CEAS manual:
+
+- http://liulab.dfci.harvard.edu/CEAS/usermanual.html
+
+History
+=======
+
+========== ======================================================================
+Version    Changes
+---------- ----------------------------------------------------------------------
+1.0.2-2    - Major updates to fix various bugs, add tests and enable ceasBW to
+             be used without an existing chromosome sizes file.
+1.0.2-1    - Modified to work with Cistrome-version of CEAS (includes additional
+             'ceasBW' program which can take bigWig input)
+1.0.2-0    - Initial version.
+========== ======================================================================
+
+Developers
+==========
+
+This tool is developed on the following GitHub repository:
+https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/ceas
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the ``package_ceas.sh`` script.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ceas_wrapper.sh	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,113 @@
+#!/bin/sh -e
+#
+# Wrapper script to run CEAS as a Galaxy tool
+#
+# This runs the Cistrome versions of CEAS, which provides two executables:
+# - ceas (same as the "official" version)
+# - ceasBW (modified version that accepts a bigwig file as input)
+#
+# Usage: ceas_wrapper.sh $BED_IN $GDB_IN $LOG_OUT $PDF_OUT $XLS_OUT [OPTIONS]
+#
+# Initialise
+CEAS=ceas
+#
+# Process command line
+echo $*
+BED_IN=$1
+GDB_IN=$2
+LOG_OUT=$3
+PDF_OUT=$4
+XLS_OUT=$5
+#
+# Initialise other variables
+EXTRA_BED_IN=
+#
+# Collect remaining args
+OPTIONS=
+while [ ! -z "$6" ] ; do
+    if [ "$6" == "--bigwig" ] ; then
+	# Bigwig input, need to use 'ceasBW'
+	CEAS=ceasBW
+	OPTIONS="$OPTIONS --bigwig"
+    elif [ "$6" == "--length" ] ; then
+	# Need a chrom sizes file
+	chrom_sizes=$7
+	if [ ! -f "$chrom_sizes" ] ; then
+	    # If chrom sizes file doesn't already exist then attempt to
+	    # download the data from UCSC
+	    echo "WARNING no file $chrom_sizes"
+	    dbkey=$(echo $(basename $chrom_sizes) | cut -d'.' -f1)
+	    if [ $dbkey == '?' ] ; then
+		# DBkey not set, this is fatal
+		echo "ERROR genome build not set, cannot get sizes for '?'" >&2
+		echo "Assign a genome build to your input dataset and rerun" >&2
+		exit 1
+	    fi
+	    # Fetch the sizes using fetchChromSizes
+	    echo -n "Attempting to download chromosome sizes for $dbkey..."
+	    chrom_sizes=$(basename $chrom_sizes)
+	    fetchChromSizes $dbkey >$chrom_sizes 2>/dev/null
+	    if [ $? -ne 0 ] ; then
+		echo "failed"
+		echo "ERROR unable to fetch data for ${dbkey}" >&2
+		echo "Please check the genome build associated with your input dataset" >&2
+		echo "or update your Galaxy instance to include an appropriate .len file" >&2
+		exit 1
+	    else
+		echo "ok"
+	    fi
+	fi
+	OPTIONS="$OPTIONS --length $chrom_sizes"
+	shift
+    else
+	OPTIONS="$OPTIONS $6"
+    fi
+    shift
+done
+#
+# Convenience variables for local files
+base_name="ceas"
+log_file=${base_name}.log
+pdf_report=${base_name}.pdf
+xls_file=${base_name}.xls
+#
+# Get CEAS version
+echo Running $CEAS
+$CEAS --version >$log_file 2>/dev/null
+#
+# Construct and run CEAS command line
+ceas_cmd="$CEAS --name $base_name $OPTIONS -g $GDB_IN -b $BED_IN"
+echo "Running $ceas_cmd"
+$ceas_cmd >>$log_file 2>&1
+status=$?
+if [ $status -ne 0 ] ; then
+    echo "Error: log file tail:"
+    tail $log_file
+    echo "ERROR $CEAS exited with non-zero code: $status" >&2
+    exit $status
+fi
+#
+# Move outputs to final destination
+if [ -e $log_file ] ; then
+    echo "Moving $log_file to $LOG_OUT"
+    /bin/mv $log_file $LOG_OUT
+else
+    echo ERROR failed to make log file >&2
+    exit 1
+fi
+if [ -e $xls_file ] ; then
+    echo "Moving $xls_file to $XLS_OUT"
+    /bin/mv $xls_file $XLS_OUT
+else
+    echo ERROR failed to generate XLS file >&2
+    exit 1
+fi
+if [ -e $pdf_report ] ; then
+    echo "Moving $pdf_report to $PDF_OUT"
+    /bin/mv $pdf_report $PDF_OUT
+else
+    echo ERROR failed to generate PDF report >&2
+    exit 1
+fi
+#
+# Done
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ceas_wrapper.xml	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,160 @@
+<tool id="ceas" name="CEAS" version="1.0.2-2">
+  <description>Annotate intervals and scores with genome features</description>
+  <requirements>
+    <requirement type="package" version="1.2.5">python_mysqldb</requirement>
+    <requirement type="package" version="0.7.1">bx_python</requirement>
+    <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
+    <requirement type="package" version="1.0">ucsc_fetchChromSizes</requirement>
+    <requirement type="package" version="3.1.2">R</requirement>
+  </requirements>
+  <version_command>ceas --version 2&gt;&amp;1 | tail -1</version_command>
+  <command interpreter="bash">ceas_wrapper.sh
+  $bed_file ${gdb_file.fields.path}
+  $log_output $pdf_report $xls_output
+  #if (str($wig_file) != 'None')
+    #if (str($wig_file.ext) == 'bigwig')
+      --bigwig $wig_file
+      --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
+    #else
+      --wig $wig_file
+    #end if
+  #end if
+  #if (str($extra_bed_file) != 'None')
+    --ebed $extra_bed_file
+  #end if
+  #if (str($span) and int(str($span)) > 0)
+    --span $span
+  #end if
+  --sizes $sizes_lower,$sizes_middle,$sizes_upper
+  --bisizes $bisizes_lower,$bisizes_upper
+  --pf-res $profiling_resolution
+  --rel-dist $relative_distance</command>
+  <inputs>
+    <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" />
+    <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true"
+	   help="If not supplied then only perform ChIP region annotation and gene-centered annotation" />
+    <param name="extra_bed_file" type="data" format="bed" label="BED file with extra regions of interest (e.g. non-coding regions)" optional="true" />
+    <param name="gdb_file" type="select" label="Gene annotation table">
+      <options from_data_table="ceas_annotations">
+      </options>
+      <filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="1" />
+      <validator type="no_options" message="No tables are available for the selected input"/>
+    </param>
+    <param name="span" type="integer"
+	   label="Span from TSS and TTS in the gene-centered annotation (bp)"
+	   help="ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates of promoter and downstream by ChIP regions (--span)" value="3000" />
+    <param name="sizes_lower" type="integer"
+	   label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)"
+	   value="1000" help=" (--sizes)" />
+    <param name="sizes_middle" type="integer"
+	   label="Middle interval for promoter/downstream sizes (bp)" value="2000"
+	   help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
+    <param name="sizes_upper" type="integer"
+	   label="Upper interval for promoter/downstream sizes (bp)" value="3000"
+	   help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
+    <param name="bisizes_lower" type="integer"
+	   label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500"
+	   help="(--bisizes)" />
+    <param name="bisizes_upper" type="integer"
+	   label="Upper interval for bidirectional-promoter sizes (bp)" value="5000"
+	   help="Values > 20000bp are automatically fixed to 20000bp (--bisizes)" />
+    <param name="profiling_resolution" type="integer"
+	   label="Wig profiling resolution (bp)" value="50"
+	   help="Warning: a number smaller than the wig interval (resolution) may cause aliasing error (--pf-res)" />
+    <param name="relative_distance" type="integer"
+	   label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000"
+	   help="(--rel-dist)" />
+  </inputs>
+  <outputs>
+    <data name="log_output" format="txt" label="CEAS on ${on_string} (log output)" />
+    <data name="pdf_report" format="pdf" label="CEAS on ${on_string} (PDF report)" />
+    <data name="xls_output" format="interval" label="CEAS on ${on_string} (XLS output)" />
+  </outputs>
+  <tests>
+    <test>
+      <!-- Test with bed input only -->
+      <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
+      <param name="gdb_file" value="galGal3_test" />
+      <output name="log_output" file="ceas_out1.log.re_match" compare="re_match"/>
+      <output name="pdf_report" file="ceas_out1.pdf" />
+      <output name="xls_output" file="ceas_out1.xls" />
+    </test>
+    <test>
+      <!-- Test with bed & very small wig input -->
+      <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
+      <param name="wig_file" value="ceas_in.wig" ftype="wig" />
+      <param name="gdb_file" value="galGal3_test" />
+      <output name="log_output" file="ceas_out2.log.re_match" compare="re_match"/>
+      <output name="pdf_report" file="ceas_out2.pdf" />
+      <output name="xls_output" file="ceas_out2.xls" />
+    </test>
+    <test>
+      <!-- Test with bed & bigwig input -->
+      <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
+      <param name="wig_file" value="ceas_in.bigwig" ftype="bigwig" />
+      <param name="gdb_file" value="galGal3_test" />
+      <output name="log_output" file="ceas_out3.log.re_match" compare="re_match"/>
+      <output name="pdf_report" file="ceas_out3.pdf" />
+      <output name="xls_output" file="ceas_out3.xls" />
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+CEAS (Cis-regulatory Element Annotation System) is a tool for characterizing genome-wide
+protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad
+binding factors. It provides statistics on ChIP enrichment at important genome features
+such as specific chromosome, promoters, gene bodies, or exons, and infers genes most
+likely to be regulated by a binding factor.
+
+CEAS also enables biologists to visualize the average ChIP enrichment signals over
+specific genomic features, allowing continuous and broad ChIP enrichment to be perceived
+which might be too subtle to detect from ChIP peaks alone.
+
+**Usage**
+
+CEAS takes the following inputs:
+
+ * BED file with discrete ChIP regions (for example, the 'summits' output from the MACS
+   peak caller)
+ * WIG or bigWIG file with a continuous ChIP enrichment signal
+ * Gene annotation table (provided as reference data)
+
+Optionally it can also take a BED file describing extra regions of interest (for example
+non-coding regions).
+
+The analysis modules are:
+
+ * **ChIP region annotation:** estimates the relative enrichment level of ChIP regions in
+   each gene feature with respect to the whole genome.
+ * **Gene-centered annotation:** identifies genes associated with ChIP regions to infer
+   the direct regulatory gene targets of the binding factor of interest.
+ * **Average signal profiling within/near important genomic features:** displays continuous
+   ChIP enrichment signal within/around important gene features to help visualize the
+   average binding patterns.
+
+**Background**
+
+This tool is compatible with the ceasBW version of CEAS from the Cistrome package
+obtained from
+
+https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
+
+(commit id d8c0751, datestamp 20140929). The CEAS code is under the
+published-packages/CEAS/ subdirectory.
+
+Cistrome data files and documentation can be found at
+
+http://liulab.dfci.harvard.edu/CEAS/index.html
+
+The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html
+  </help>
+  <citations>
+    <!--
+    See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+    Can be either DOI or Bibtex
+    Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
+    -->
+    <citation type="doi">10.1093/bioinformatics/btp479</citation>
+  </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_ceas_fetch_annotations.py	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,153 @@
+#!/usr/bin/env python
+#
+
+import sys
+import os
+import subprocess
+import tempfile
+import optparse
+import urllib2
+import gzip
+import shutil
+
+from galaxy.util.json import from_json_string, to_json_string
+
+# Download file from specified URL and put into local subdir
+
+if __name__ == '__main__':
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    options,args = parser.parse_args()
+    print "options: %s" % options
+    print "args   : %s" % args
+    if len(args) != 2:
+        p.error("Need to supply JSON file name and description text")
+
+    # Read the JSON supplied from the data manager tool
+    # Results from this program will be returned via the
+    # same file
+    jsonfile = args[0]
+    params = from_json_string(open(jsonfile).read() )
+    print "%s" % params
+
+    # Extract the data from the input JSON
+    # See https://wiki.galaxyproject.org/Admin/Tools/DataManagers/HowTo/Define?highlight=%28\bAdmin%2FTools%2FDataManagers\b%29
+    # for example of JSON
+    #
+    # We want the values set in the data manager XML
+    dbkey = params['param_dict']['dbkey']
+    description = args[1].strip()
+    identifier = params['param_dict']['unique_id'].strip()
+    # Where to put the output file
+    # Nb we have to make this ourselves, it doesn't exist by default
+    target_dir = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_dir)
+
+    method = params['param_dict']['reference_source']['reference_source_selector']
+
+    # Dictionary for returning to data manager
+    data_manager_dict = {}
+    data_manager_dict['data_tables'] = dict()
+
+    # Download from URL
+    if method == 'web':
+        url = params['param_dict']['reference_source']['annotation_url']
+        print "Downloading: %s" % url
+        annotation_file_name = os.path.basename(url)
+        annotation_file_path = os.path.join(target_dir,annotation_file_name)
+        print "Annotation file name: %s" % annotation_file_name
+        print "Annotation file path: %s" % annotation_file_path
+        open(annotation_file_path,'wb').write(urllib2.urlopen(url).read())
+        if annotation_file_name.endswith('.gz'):
+            # Uncompress
+            uncompressed_file = annotation_file_path[:-3]
+            open(uncompressed_file,'wb').write(gzip.open(annotation_file_path,'rb').read())
+            # Remove gzipped file
+            os.remove(annotation_file_path)
+            annotation_file_name = os.path.basename(uncompressed_file)
+            annotation_file_path = uncompressed_file
+        # Update the identifier and description
+        if not identifier:
+            identifier = "%s_ceas_web" % dbkey
+        if not description:
+            description = "%s (%s)" % (os.path.splitext(annotation_file_name)[0],dbkey)
+        # Update the output dictionary
+        data_manager_dict['data_tables']['ceas_annotations'] = {
+            'value': identifier,
+            'dbkey': dbkey,
+            'name': description,
+            'path': annotation_file_name,
+        }
+    elif method == 'server':
+        # Pull in a file from the server
+        filename = params['param_dict']['reference_source']['annotation_filename']
+        create_symlink = params['param_dict']['reference_source']['create_symlink']
+        print "Canonical gene list file name: %s" % filename
+        print "Create symlink: %s" % create_symlink
+        target_filename = os.path.join(target_dir,os.path.basename(filename))
+        if create_symlink == 'copy_file':
+            shutil.copyfile(filename,target_filename)
+        else:
+            os.symlink(filename,target_filename)
+        # Update the identifier and description
+        if not identifier:
+            identifier = "%s_%s" % (dbkey,
+                                    os.path.splitext(os.path.basename(filename))[0])
+        if not description:
+            description = "%s: %s" % (dbkey,
+                                      os.path.splitext(os.path.basename(filename))[0])
+        # Update the output dictionary
+        data_manager_dict['data_tables']['ceas_annotations'] = {
+            'value': identifier,
+            'dbkey': dbkey,
+            'name': description,
+            'path': os.path.basename(filename),
+        }
+    elif method == 'from_wig':
+        # Make a reference file from a wig file
+        wig_file = params['param_dict']['reference_source']['wig_file']
+        gene_annotation = params['param_dict']['reference_source']['gene_annotation']
+        target_filename = os.path.join(target_dir,"%s_%s.%s" % (dbkey,
+                                                                os.path.basename(wig_file),
+                                                                gene_annotation))
+        print "Wig file: %s" % wig_file
+        print "Gene annotation: %s" % gene_annotation
+        print "Output file: %s" % os.path.basename(target_filename)
+        # Make a working directory
+        working_dir = tempfile.mkdtemp()
+        # Collect stderr in a file for reporting later
+        stderr_filen = tempfile.NamedTemporaryFile().name
+        # Build the command to run
+        cmd = "build_genomeBG -d %s -g %s -w %s -o %s" % (dbkey,
+                                                          gene_annotation,
+                                                          wig_file,
+                                                          target_filename)
+        print "Running %s" %  cmd
+        proc = subprocess.Popen(args=cmd,shell=True,cwd=working_dir,
+                                stderr=open(stderr_filen,'wb'))
+        proc.wait()
+        # Copy stderr to stdout
+        with open(stderr_filen,'r') as fp:
+            sys.stdout.write(fp.read())
+        # Update identifier and description
+        if not identifier:
+            identifier = "%s_%s_%s" % (dbkey,
+                                       gene_annotation,
+                                       os.path.basename(wig_file))
+        if not description:
+            description = "%s %s from %s" % (dbkey,
+                                             gene_annotation,
+                                             os.path.basename(wig_file))
+        # Update the output dictionary
+        data_manager_dict['data_tables']['ceas_annotations'] = {
+            'value': identifier,
+            'dbkey': dbkey,
+            'name': description,
+            'path': os.path.basename(target_filename),
+        }
+    else:
+        raise NotImplementedError("Method '%s' not implemented" % method)
+
+    #save info to json file
+    open(jsonfile,'wb').write(to_json_string(data_manager_dict))
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_ceas_fetch_annotations.xml	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,95 @@
+<tool id="data_manager_fetch_ceas_annotations" name="Fetch CEAS annotation" version="0.0.1" tool_type="manage_data">
+    <requirements>
+      <requirement type="package" version="1.2.5">python_mysqldb</requirement>
+      <requirement type="package" version="0.7.1">bx_python</requirement>
+      <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
+    </requirements>
+    <description>Fetch and install annotation databases for CEAS</description>
+    <command interpreter="python">data_manager_ceas_fetch_annotations.py
+    "${out_file}"
+    "${description}"</command>
+    <inputs>
+        <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" />
+	<param type="text" name="unique_id" label="Internal identifier"
+	       help="Identifier string to associate with the annotation e.g. 'mm9_generic'" />
+        <param type="text" name="description" value="" size="50"
+	       label="Description of annotation"
+	       help="Text that will be displayed to the user when selecting which annotation to use" />
+        <conditional name="reference_source">
+          <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+            <option value="web" selected="True">CEAS website</option>
+            <option value="server">File on the server</option>
+	    <option value="from_wig">Generated from wig file</option>
+          </param>
+          <when value="web">
+            <param type="select" name="annotation_url">
+	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg18.refGene.gz">hg18</option>
+	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/hg19.refGene.gz">hg19</option>
+	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm8.refGene.gz">mm8</option>
+	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/mm9.refGene.gz">mm9</option>
+	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm2.refGene.gz">dm2</option>
+	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/dm3.refGene.gz">dm3</option>
+	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce4.refGene.gz">ce4</option>
+	      <option value="http://liulab.dfci.harvard.edu/CEAS/src/ce6.refGene.gz">ce6</option>
+	    </param>
+          </when>
+          <when value="server">
+            <param type="text" name="annotation_filename" value="" size="50"
+		   label="Full path to CEAS annotation table file on disk" optional="False" />
+            <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" />
+          </when>
+	  <when value="from_wig">
+	    <param type="data" format="wig" name="wig_file" value=""
+		   label="Wig file to use for the background genome annotation"
+		   help="Will be used as input to build_genomeBG" />
+	    <param type="select" name="gene_annotation"
+		   label="Gene annotation from UCSC">
+	      <option value="refGene">refGene</option>
+	    </param>
+	  </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+	  <!-- No tests defined, yet -->
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What it does**
+
+Adds a CEAS gene annotation table file to the *ceas_annotations"* data table. The
+database file can be downloaded from the CEAS website, imported from a file on the
+Galaxy server, or generated from a ``wig`` file in a Galaxy history.
+
+**Notice:** If you leave the identifier or description blank then they will be
+generated automatically. 
+
+------
+
+.. class:: infomark
+
+**Fetching, uploading or creating gene annotation table files**
+
+The gene annotation table files are SQLite database files which are on the CEAS website:
+
+ - http://liulab.dfci.harvard.edu/CEAS/usermanual.html
+
+The data manager allows you to fetch a pre-built table from the CEAS website; note
+that these are based on the ``RefSeq`` annotation and are only available for a subset
+of genome builds.
+
+To create an annotation table for a different genome build or a different annotation,
+use the *Generated from wig* file option. This runs the CEAS utility ``build_genomeBG``
+to make a custom table from a wig file, which represents the genome background (e.g.
+a wig file created from the ``control lambda`` bedgraph file output from MACS2).
+
+Alternatively if you already have an existing custom annotation file then this can be
+imported from a path on the Galaxy server.
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<data_managers>
+    <data_manager tool_file="data_manager/data_manager_ceas_fetch_annotations.xml" id="ceas_fetch_annotations">
+        <data_table name="ceas_annotations">
+            <output>
+	      <column name="value" />
+              <column name="dbkey" />
+              <column name="name" />
+              <column name="path" output_ref="out_file" >
+                <move type="file">
+                  <source>${path}</source>
+                  <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">ceas/${dbkey}/${path}</target>
+                </move>
+                <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/ceas/${dbkey}/${path}</value_translation>
+                <value_translation type="function">abspath</value_translation>
+              </column>
+            </output>
+        </data_table>
+    </data_manager>
+</data_managers>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas.loc	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,1 @@
+galGal3_test	galGal3	galGal3	${__HERE__}/galGal3.refGene
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_in.bed	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,1 @@
+chr26	4119129	4119130	test_MACS2.1.0_peak_1	2.51561
Binary file test-data/ceas_in.bigwig has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_in.wig	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,4312 @@
+track type=wiggle_0 name="test_MACS2.1.0_treat_pileup.bdg" description="test_MACS2.1.0_treat_pileup.bdg" visibility=full
+fixedStep chrom=chr26 start=0 step=1000 span=1
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out1.log	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,184 @@
+ceas -- 0.9.9.7 (package version 1.0.2)
+INFO  @ Tue, 23 Jun 2015 09:12:22: 
+# ARGUMENTS: 
+# name = ceas
+# gene annotation table = galGal3.refGene
+# BED file = ceas_in.bed
+# WIG file = None
+# extra BED file = None
+# ChIP annotation = On
+# gene-centered annotation =  On
+# average profiling = Off
+# dump profiles = Off
+# re-annotation for genome background (ChIP region annotation) = False
+# promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
+# downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
+# bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
+# span size (gene-centered annotation) = 3000 bp 
+INFO  @ Tue, 23 Jun 2015 09:12:22: #1 read the gene table... 
+INFO  @ Tue, 23 Jun 2015 09:12:22: #2 read the bed file of ChIP regions... 
+INFO  @ Tue, 23 Jun 2015 09:12:22: #3 perform gene-centered annotation... 
+INFO  @ Tue, 23 Jun 2015 09:12:22: #4 See ceas.xls for gene-centered annotation! 
+INFO  @ Tue, 23 Jun 2015 09:12:22: #5 read the pre-computed genome bg annotation... 
+INFO  @ Tue, 23 Jun 2015 09:12:22: #6 perform ChIP region annotation... 
+INFO  @ Tue, 23 Jun 2015 09:12:22: #7 write a R script of ChIP region annotation... 
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-redhat-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+  Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # ARGUMENTS: 
+> # name = ceas
+> # gene annotation table = galGal3.refGene
+> # BED file = ceas_in.bed
+> # WIG file = None
+> # extra BED file = None
+> # ChIP annotation = On
+> # gene-centered annotation =  On
+> # average profiling = Off
+> # dump profiles = Off
+> # re-annotation for genome background (ChIP region annotation) = False
+> # promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
+> # downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
+> # bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
+> # span size (gene-centered annotation) = 3000 bp
+> pdf("ceas.pdf",height=11.5,width=8.5)
+> 
+> # 09:12:22 Tue, 23 Jun 2015
+> # 
+> # ChIP annotation
+> # 
+> 
+> 
+> # 
+> # Chromosomal Distribution
+> # 
+> 
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> r0<-c(100.0)
+> r1<-c(100.0)
+> height<-rbind(r0,r1)
+> names=c("26")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=TRUE,col=c("#5FA1C1","#EB9D86"),main="Chromosomal Distribution of ChIP Regions",xlab="Percentage %",ylab="Chromosome",border=FALSE,xlim=c(0.000000,183.333333),cex.names=1)
+> text(x=c(100.0),y=mp[1,],label=c("100.0 %"),pos=4,offset=0.2,cex=0.9)
+> text(x=c(100.0),y=mp[2,],label=c("100.0 % (<=4.9e-324)"),pos=4,offset=0.2,cex=0.9)
+> legend("right",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> 
+> # 
+> # Promoter,Bipromoter,Downstream, Gene and Regions of interest
+> # 
+> 
+> par(mfrow=c(4, 1),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> r0<-c(1.8532425688606797, 3.616851183410451, 5.322318854623416)
+> r1<-c(0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=1000 bp","<=2000 bp","<=3000 bp")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Promoter",ylab="Percentage %",border=FALSE,ylim=c(0.000000,9.757585),cex.names=1)
+> text(x=mp[1,],y=c(1.8532425688606797, 3.616851183410451, 5.322318854623416),label=c("1.9 %","3.6 %","5.3 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0),label=c("0.000 %
++ (0.981)","0.000 %
++ (0.964)","0.000 %
++ (0.947)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(0.03876062889120376, 0.03876062889120376)
+> r1<-c(0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=2500 bp","<=5000 bp")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Bidirectional Promoter",ylab="Percentage %",border=FALSE,ylim=c(0.000000,0.071061),cex.names=1)
+> text(x=mp[1,],y=c(0.03876062889120376, 0.03876062889120376),label=c("0.04 %","0.04 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0),label=c("0.000 %
++ (1.000)","0.000 %
++ (1.000)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(1.8290171758036773, 3.4690762857627364, 4.980740812519683)
+> r1<-c(0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=1000 bp","<=2000 bp","<=3000 bp")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Downstream",ylab="Percentage %",border=FALSE,ylim=c(0.000000,9.131358),cex.names=1)
+> text(x=mp[1,],y=c(1.8290171758036773, 3.4690762857627364, 4.980740812519683),label=c("1.8 %","3.5 %","5.0 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0),label=c("0.000 %
++ (0.982)","0.000 %
++ (0.965)","0.000 %
++ (0.950)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(0.2034933016788197, 1.3978051793890356, 2.359553283752029, 19.734005184234114, 23.694856949054)
+> r1<-c(0.0, 0.0, 0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("5'UTR","3'UTR","Coding Exon","Intron","All")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Gene",ylab="Percentage %",border=FALSE,ylim=c(0.000000,43.440571),cex.names=1)
+> text(x=mp[1,],y=c(0.2034933016788197, 1.3978051793890356, 2.359553283752029, 19.734005184234114, 23.694856949054),label=c("0.2 %","1.4 %","2.4 %","19.7 %","23.7 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0, 0.0, 0.0),label=c("0.000 %
++ (0.998)","0.000 %
++ (0.986)","0.000 %
++ (0.976)","0.000 %
++ (0.803)","0.000 %
++ (0.763)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> 
+> # 
+> # Distribution of Genome and ChIP regions over cis-regulatory element
+> # Note that the x may be modified for better graphics in case a value is too small
+> # Thus, look at the labels of the pie chart to get the real percentage values
+> # 
+> 
+> par(mfcol=c(2, 2),mar=c(3, 3, 4, 2.8),oma=c(4, 2, 4, 2))
+> x<-c(0.018532,0.017055,0.016037,0.017830,0.015092,0.014051,0.010000,0.013833,0.023014,0.192592,0.670292)
+> pie(x=x,labels=c("1.9 %","1.7 %","1.6 %","1.8 %","1.5 %","1.4 %","0.2 %","1.4 %","2.3 %","19.3 %","67.0 %"),main="Genome",col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),clockwise=TRUE,border=FALSE,radius=0.9,cex=0.8,init.angle=90,density=100)
+> x<-c(0.000000,1.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
+> legend("top",legend=c("Promoter (<=1000 bp): 1.9 %","Promoter (1000-2000 bp): 1.7 %","Promoter (2000-3000 bp): 1.6 %","Downstream (<=1000 bp): 1.8 %","Downstream (1000-2000 bp): 1.5 %","Downstream (2000-3000 bp): 1.4 %","5'UTR: 0.2 %","3'UTR: 1.4 %","Coding exon: 2.3 %","Intron: 19.3 %","Distal intergenic: 67.0 %"),col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),pch=15,bty="n")
+> x<-c(0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,1.000000)
+> pie(x=x,labels=c("0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","100.0 %"),main="ChIP",col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),clockwise=TRUE,border=FALSE,radius=0.9,cex=0.8,init.angle=90,density=100)
+> x<-c(0.000000,1.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
+> legend("top",legend=c("Promoter (<=1000 bp): 0.000 %","Promoter (1000-2000 bp): 0.000 %","Promoter (2000-3000 bp): 0.000 %","Downstream (<=1000 bp): 0.000 %","Downstream (1000-2000 bp): 0.000 %","Downstream (2000-3000 bp): 0.000 %","5'UTR: 0.000 %","3'UTR: 0.000 %","Coding exon: 0.000 %","Intron: 0.000 %","Distal intergenic: 100.0 %"),col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),pch=15,bty="n")
+> 
+> # 
+> # ChIP regions over the genome
+> # 
+> 
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> layout(matrix(c(1, 0, 2, 2), 2, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 5))
+> x<-c(0.000000,2.515610)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="Distribution of Peak Heights",xlab="",ylab="",xlim=c(0.000000,2.515610),ylim=c(0.000000,1.000000),frame=FALSE,xaxt="s",yaxt="n",cex=0.9)
+> x<-c(0.000000,2.515610,2.515610,0.000000)
+> y<-c(0.000000,0.000000,1.000000,1.000000)
+> polygon(x,y,col=c("black"))
+> x <- c(0.000000,0.169726,0.339451,0.509177,0.678903,0.848628,1.018354,1.188079,1.357805,1.527531,1.697256,1.866982,2.036708,2.206433,2.376159)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.800000)
+> lines(x, y,xlim=c(0, 2.51561),ylim=c(0, 1),type="l",col=c("cyan"),lwd=2)
+> x<-c(4119129.000000,4119130.000000)
+> y<-c(0.855556,1.144444)
+> plot(x, y,type="n",main="ChIP Regions (Peaks) over Chromosomes",xlab="Chromosome Size (bp)",ylab="Chromosome",xlim=c(4119129.000000,4119130.000000),ylim=c(0.855556,1.144444),frame=FALSE,xaxt="s",yaxt="n")
+> start <- c(4119129)
+> end <- c(4119130)
+> vals <- c(2.51561)
+> vals[vals > 2.51561] <- 2.51561
+> vals[vals < 0] <- 0
+> heights <- 0.288889 * ((vals - 0)/(2.51561 - 0)) + 0.855555555556
+> for (i in 1:length(heights)) {
++ 	polygon(x=c(start[i], end[i], end[i], start[i]), y=c(0.855555555556, 0.855555555556, heights[i], heights[i]), col=c("#CC0000"), border=c("#CC0000"))
++ }
+> mtext("26",side=2,line=0,outer=FALSE,at=1.0)
+> dev.off()
+null device 
+          1 
+> 
+INFO  @ Tue, 23 Jun 2015 09:12:22: #... cong! See ceas.pdf for the graphical results of CEAS! 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out1.log.re_match	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,184 @@
+ceas\ \-\-\ 0\.9\.9\.7\ \(package\ version\ 1\.0\.2\)
+INFO\ \ \@\ .*
+\#\ ARGUMENTS\:\ 
+\#\ name\ \=\ ceas
+\#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
+\#\ BED\ file\ \=\ .*
+\#\ WIG\ file\ \=\ None
+\#\ extra\ BED\ file\ \=\ None
+\#\ ChIP\ annotation\ \=\ On
+\#\ gene\-centered\ annotation\ \=\ \ On
+\#\ average\ profiling\ \=\ Off
+\#\ dump\ profiles\ \=\ Off
+\#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
+\#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
+\#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp\ 
+INFO\ \ \@\ .*\ \#1\ read\ the\ gene\ table\.\.\.\ 
+INFO\ \ \@\ .*\ \#2\ read\ the\ bed\ file\ of\ ChIP\ regions\.\.\.\ 
+INFO\ \ \@\ .*\ \#3\ perform\ gene\-centered\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#4\ See\ ceas\.xls\ for\ gene\-centered\ annotation\!\ 
+INFO\ \ \@\ .*\ \#5\ read\ the\ pre\-computed\ genome\ bg\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#6\ perform\ ChIP\ region\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#7\ write\ a\ R\ script\ of\ ChIP\ region\ annotation\.\.\.\ 
+
+R\ version\ 3\.1\.2\ \(2014\-10\-31\)\ \-\-\ \"Pumpkin\ Helmet\"
+Copyright\ \(C\)\ 2014\ The\ R\ Foundation\ for\ Statistical\ Computing
+Platform\:\ .*
+
+R\ is\ free\ software\ and\ comes\ with\ ABSOLUTELY\ NO\ WARRANTY\.
+You\ are\ welcome\ to\ redistribute\ it\ under\ certain\ conditions\.
+Type\ \'license\(\)\'\ or\ \'licence\(\)\'\ for\ distribution\ details\.
+
+\ \ Natural\ language\ support\ but\ running\ in\ an\ English\ locale
+
+R\ is\ a\ collaborative\ project\ with\ many\ contributors\.
+Type\ \'contributors\(\)\'\ for\ more\ information\ and
+\'citation\(\)\'\ on\ how\ to\ cite\ R\ or\ R\ packages\ in\ publications\.
+
+Type\ \'demo\(\)\'\ for\ some\ demos\,\ \'help\(\)\'\ for\ on\-line\ help\,\ or
+\'help\.start\(\)\'\ for\ an\ HTML\ browser\ interface\ to\ help\.
+Type\ \'q\(\)\'\ to\ quit\ R\.
+
+\>\ \#\ ARGUMENTS\:\ 
+\>\ \#\ name\ \=\ ceas
+\>\ \#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
+\>\ \#\ BED\ file\ \=\ .*
+\>\ \#\ WIG\ file\ \=\ None
+\>\ \#\ extra\ BED\ file\ \=\ None
+\>\ \#\ ChIP\ annotation\ \=\ On
+\>\ \#\ gene\-centered\ annotation\ \=\ \ On
+\>\ \#\ average\ profiling\ \=\ Off
+\>\ \#\ dump\ profiles\ \=\ Off
+\>\ \#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
+\>\ \#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\>\ \#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\>\ \#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
+\>\ \#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp
+\>\ pdf\(\"ceas\.pdf\"\,height\=11\.5\,width\=8\.5\)
+\>\ 
+\>\ \#\ .*
+\>\ \#\ 
+\>\ \#\ ChIP\ annotation
+\>\ \#\ 
+\>\ 
+\>\ 
+\>\ \#\ 
+\>\ \#\ Chromosomal\ Distribution
+\>\ \#\ 
+\>\ 
+\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ r0\<\-c\(100\.0\)
+\>\ r1\<\-c\(100\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"26\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=TRUE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Chromosomal\ Distribution\ of\ ChIP\ Regions\"\,xlab\=\"Percentage\ \%\"\,ylab\=\"Chromosome\"\,border\=FALSE\,xlim\=c\(0\.000000\,183\.333333\)\,cex\.names\=1\)
+\>\ text\(x\=c\(100\.0\)\,y\=mp\[1\,\]\,label\=c\(\"100\.0\ \%\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
+\>\ text\(x\=c\(100\.0\)\,y\=mp\[2\,\]\,label\=c\(\"100\.0\ \%\ \(\<\=4\.9e\-324\)\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
+\>\ legend\(\"right\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ 
+\>\ \#\ 
+\>\ \#\ Promoter\,Bipromoter\,Downstream\,\ Gene\ and\ Regions\ of\ interest
+\>\ \#\ 
+\>\ 
+\>\ par\(mfrow\=c\(4\,\ 1\)\,mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ r0\<\-c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.757585\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)\,label\=c\(\"1\.9\ \%\"\,\"3\.6\ \%\"\,\"5\.3\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(0\.981\)\"\,\"0\.000\ \%
+\+\ \(0\.964\)\"\,\"0\.000\ \%
+\+\ \(0\.947\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ r0\<\-c\(0\.03876062889120376\,\ 0\.03876062889120376\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"\<\=2500\ bp\"\,\"\<\=5000\ bp\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Bidirectional\ Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,0\.071061\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(0\.03876062889120376\,\ 0\.03876062889120376\)\,label\=c\(\"0\.04\ \%\"\,\"0\.04\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(1\.000\)\"\,\"0\.000\ \%
+\+\ \(1\.000\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ r0\<\-c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Downstream\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.131358\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)\,label\=c\(\"1\.8\ \%\"\,\"3\.5\ \%\"\,\"5\.0\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(0\.982\)\"\,\"0\.000\ \%
+\+\ \(0\.965\)\"\,\"0\.000\ \%
+\+\ \(0\.950\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ r0\<\-c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"5\'UTR\"\,\"3\'UTR\"\,\"Coding\ Exon\"\,\"Intron\"\,\"All\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Gene\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,43\.440571\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)\,label\=c\(\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.4\ \%\"\,\"19\.7\ \%\"\,\"23\.7\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(0\.998\)\"\,\"0\.000\ \%
+\+\ \(0\.986\)\"\,\"0\.000\ \%
+\+\ \(0\.976\)\"\,\"0\.000\ \%
+\+\ \(0\.803\)\"\,\"0\.000\ \%
+\+\ \(0\.763\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ 
+\>\ \#\ 
+\>\ \#\ Distribution\ of\ Genome\ and\ ChIP\ regions\ over\ cis\-regulatory\ element
+\>\ \#\ Note\ that\ the\ x\ may\ be\ modified\ for\ better\ graphics\ in\ case\ a\ value\ is\ too\ small
+\>\ \#\ Thus\,\ look\ at\ the\ labels\ of\ the\ pie\ chart\ to\ get\ the\ real\ percentage\ values
+\>\ \#\ 
+\>\ 
+\>\ par\(mfcol\=c\(2\,\ 2\)\,mar\=c\(3\,\ 3\,\ 4\,\ 2\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ x\<\-c\(0\.018532\,0\.017055\,0\.016037\,0\.017830\,0\.015092\,0\.014051\,0\.010000\,0\.013833\,0\.023014\,0\.192592\,0\.670292\)
+\>\ pie\(x\=x\,labels\=c\(\"1\.9\ \%\"\,\"1\.7\ \%\"\,\"1\.6\ \%\"\,\"1\.8\ \%\"\,\"1\.5\ \%\"\,\"1\.4\ \%\"\,\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.3\ \%\"\,\"19\.3\ \%\"\,\"67\.0\ \%\"\)\,main\=\"Genome\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
+\>\ x\<\-c\(0\.000000\,1\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 1\.9\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 1\.7\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 1\.6\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 1\.8\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 1\.5\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 1\.4\ \%\"\,\"5\'UTR\:\ 0\.2\ \%\"\,\"3\'UTR\:\ 1\.4\ \%\"\,\"Coding\ exon\:\ 2\.3\ \%\"\,\"Intron\:\ 19\.3\ \%\"\,\"Distal\ intergenic\:\ 67\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ x\<\-c\(0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,1\.000000\)
+\>\ pie\(x\=x\,labels\=c\(\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"100\.0\ \%\"\)\,main\=\"ChIP\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
+\>\ x\<\-c\(0\.000000\,1\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"5\'UTR\:\ 0\.000\ \%\"\,\"3\'UTR\:\ 0\.000\ \%\"\,\"Coding\ exon\:\ 0\.000\ \%\"\,\"Intron\:\ 0\.000\ \%\"\,\"Distal\ intergenic\:\ 100\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ 
+\>\ \#\ 
+\>\ \#\ ChIP\ regions\ over\ the\ genome
+\>\ \#\ 
+\>\ 
+\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ layout\(matrix\(c\(1\,\ 0\,\ 2\,\ 2\)\,\ 2\,\ 2\,\ byrow\ \=\ TRUE\)\,widths\=c\(1\,\ 1\)\,heights\=c\(1\,\ 5\)\)
+\>\ x\<\-c\(0\.000000\,2\.515610\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"Distribution\ of\ Peak\ Heights\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(0\.000000\,2\.515610\)\,ylim\=c\(0\.000000\,1\.000000\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\,cex\=0\.9\)
+\>\ x\<\-c\(0\.000000\,2\.515610\,2\.515610\,0\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,1\.000000\,1\.000000\)
+\>\ polygon\(x\,y\,col\=c\(\"black\"\)\)
+\>\ x\ \<\-\ c\(0\.000000\,0\.169726\,0\.339451\,0\.509177\,0\.678903\,0\.848628\,1\.018354\,1\.188079\,1\.357805\,1\.527531\,1\.697256\,1\.866982\,2\.036708\,2\.206433\,2\.376159\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.800000\)
+\>\ lines\(x\,\ y\,xlim\=c\(0\,\ 2\.51561\)\,ylim\=c\(0\,\ 1\)\,type\=\"l\"\,col\=c\(\"cyan\"\)\,lwd\=2\)
+\>\ x\<\-c\(4119129\.000000\,4119130\.000000\)
+\>\ y\<\-c\(0\.855556\,1\.144444\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"ChIP\ Regions\ \(Peaks\)\ over\ Chromosomes\"\,xlab\=\"Chromosome\ Size\ \(bp\)\"\,ylab\=\"Chromosome\"\,xlim\=c\(4119129\.000000\,4119130\.000000\)\,ylim\=c\(0\.855556\,1\.144444\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\)
+\>\ start\ \<\-\ c\(4119129\)
+\>\ end\ \<\-\ c\(4119130\)
+\>\ vals\ \<\-\ c\(2\.51561\)
+\>\ vals\[vals\ \>\ 2\.51561\]\ \<\-\ 2\.51561
+\>\ vals\[vals\ \<\ 0\]\ \<\-\ 0
+\>\ heights\ \<\-\ 0\.288889\ \*\ \(\(vals\ \-\ 0\)\/\(2\.51561\ \-\ 0\)\)\ \+\ 0\.855555555556
+\>\ for\ \(i\ in\ 1\:length\(heights\)\)\ \{
+\+\ \	polygon\(x\=c\(start\[i\]\,\ end\[i\]\,\ end\[i\]\,\ start\[i\]\)\,\ y\=c\(0\.855555555556\,\ 0\.855555555556\,\ heights\[i\]\,\ heights\[i\]\)\,\ col\=c\(\"\#CC0000\"\)\,\ border\=c\(\"\#CC0000\"\)\)
+\+\ \}
+\>\ mtext\(\"26\"\,side\=2\,line\=0\,outer\=FALSE\,at\=1\.0\)
+\>\ dev\.off\(\)
+null\ device\ 
+\ \ \ \ \ \ \ \ \ \ 1\ 
+\>\ 
+INFO\ \ \@\ .*\ \#\.\.\.\ cong\!\ See\ ceas\.pdf\ for\ the\ graphical\ results\ of\ CEAS\!\ 
Binary file test-data/ceas_out1.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out1.xls	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,133 @@
+# RefSeq: RefSeq ID
+# chr: chromosome of a RefSeq gene
+# txStart: 5' end of a RefSeq gene
+# txEnd: 3' end site of a RefSeq gene
+# strand: strand of a RefSeq gene
+# dist u TSS: Distance to the nearest ChIP region's center upstream of transcription start site (bp)
+# dist d TSS: Distance to the nearest ChIP region's center downstream of transcription start site (bp)
+# dist u TTS: Distance to the nearest ChIP region's center upstream of transcription end site (bp)
+# dist d TTS: Distance to the nearest ChIP region's center downstream of transcription end (bp)
+# 3000bp u TSS: Occupancy rate of ChIP region in 3000bp upstream of transcription start site (0.0 - 1.0)
+# 3000bp d TSS: Occupancy rate of ChIP region in 3000bp downstream of transcription start site (0.0 - 1.0)
+# 1/3 gene: Occupancy rate of ChIP region in 1/3 gene (0.0 - 1.0)
+# 2/3 gene: Occupancy rate of ChIP region in 2/3 gene (0.0 - 1.0)
+# 3/3 gene: Occupancy rate of ChIP region in 3/3 gene (0.0 - 1.0)
+# 3000bp d TTS: Occupancy rate of ChIP region in 3000bp downstream of transcriptino end (0.0 - 1.0)
+# exons: Occupancy rate of ChIP regions in exons (0.0-1.0)
+# Note that txStart and txEnd indicate 5' and 3' ends of genes whereas TSS and TTS transcription start and end sites in consideration of strand.
+#name	chr	txStart	txEnd	strand	dist u TSS	dist d TSS	dist u TTS	dist d TTS	3000bp u TSS	3000bp d TSS	1/3 gene	2/3 gene	3/3 gene	3000bp d TTS	exons
+NM_001031576	chr26	19281	27136	+	NA	4099848	NA	4091993	0	0	0	0	0	0	0
+NM_204615	chr26	57466	61594	-	4057535	NA	4061663	NA	0	0	0	0	0	0	0
+NM_001005431	chr26	65800	76175	-	4042954	NA	4053329	NA	0	0	0	0	0	0	0
+NM_001145491	chr26	91618	92166	-	4026963	NA	4027511	NA	0	0	0	0	0	0	0
+NM_204398	chr26	93069	97423	+	NA	4026060	NA	4021706	0	0	0	0	0	0	0
+NM_001305147	chr26	254661	282571	+	NA	3864468	NA	3836558	0	0	0	0	0	0	0
+NM_001305148	chr26	254661	282571	+	NA	3864468	NA	3836558	0	0	0	0	0	0	0
+NM_001012868	chr26	350397	355252	-	3763877	NA	3768732	NA	0	0	0	0	0	0	0
+NM_001031030	chr26	479573	493561	+	NA	3639556	NA	3625568	0	0	0	0	0	0	0
+NM_001305140	chr26	520705	526012	+	NA	3598424	NA	3593117	0	0	0	0	0	0	0
+NM_001031029	chr26	537101	565572	+	NA	3582028	NA	3553557	0	0	0	0	0	0	0
+NM_205248	chr26	537250	760479	+	NA	3581879	NA	3358650	0	0	0	0	0	0	0
+NM_204727	chr26	662969	683066	-	3436063	NA	3456160	NA	0	0	0	0	0	0	0
+NR_105475	chr26	669012	669122	-	3450007	NA	3450117	NA	0	0	0	0	0	0	0
+NM_205449	chr26	785617	794076	+	NA	3333512	NA	3325053	0	0	0	0	0	0	0
+NM_204681	chr26	897458	902049	-	3217080	NA	3221671	NA	0	0	0	0	0	0	0
+NM_001278156	chr26	905313	917094	-	3202035	NA	3213816	NA	0	0	0	0	0	0	0
+NM_204184	chr26	960209	964268	-	3154861	NA	3158920	NA	0	0	0	0	0	0	0
+NM_204316	chr26	974223	991244	+	NA	3144906	NA	3127885	0	0	0	0	0	0	0
+NM_001031028	chr26	993815	1003847	-	3115282	NA	3125314	NA	0	0	0	0	0	0	0
+NM_001006392	chr26	1024606	1047756	-	3071373	NA	3094523	NA	0	0	0	0	0	0	0
+NM_001039596	chr26	1073550	1080033	-	3039096	NA	3045579	NA	0	0	0	0	0	0	0
+NM_001031027	chr26	1090460	1096137	+	NA	3028669	NA	3022992	0	0	0	0	0	0	0
+NM_001031026	chr26	1096566	1104751	-	3014378	NA	3022563	NA	0	0	0	0	0	0	0
+NM_001030913	chr26	1122296	1132596	+	NA	2996833	NA	2986533	0	0	0	0	0	0	0
+NM_001171886	chr26	1220031	1222791	-	2896338	NA	2899098	NA	0	0	0	0	0	0	0
+NM_205054	chr26	1229703	1232833	+	NA	2889426	NA	2886296	0	0	0	0	0	0	0
+NM_204462	chr26	1234686	1236536	-	2882593	NA	2884443	NA	0	0	0	0	0	0	0
+NM_204463	chr26	1265724	1267989	-	2851140	NA	2853405	NA	0	0	0	0	0	0	0
+NM_001030378	chr26	1289091	1290386	-	2828743	NA	2830038	NA	0	0	0	0	0	0	0
+NM_001195554	chr26	1382510	1388447	+	NA	2736619	NA	2730682	0	0	0	0	0	0	0
+NM_001012548	chr26	1406905	1428443	+	NA	2712224	NA	2690686	0	0	0	0	0	0	0
+NR_031486	chr26	1442696	1442779	-	2676350	NA	2676433	NA	0	0	0	0	0	0	0
+NR_031487	chr26	1442896	1442979	-	2676150	NA	2676233	NA	0	0	0	0	0	0	0
+NM_205250	chr26	1472137	1474003	+	NA	2646992	NA	2645126	0	0	0	0	0	0	0
+NR_105486	chr26	1566398	1566508	-	2552621	NA	2552731	NA	0	0	0	0	0	0	0
+NM_001160320	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001004709	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160324	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001004493	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160323	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160322	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160321	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001004395	chr26	1776431	1800083	+	NA	2342698	NA	2319046	0	0	0	0	0	0	0
+NM_001030914	chr26	1811042	1820368	-	2298761	NA	2308087	NA	0	0	0	0	0	0	0
+NM_204506	chr26	1823407	1843085	-	2276044	NA	2295722	NA	0	0	0	0	0	0	0
+NR_031488	chr26	1925941	1926037	-	2193092	NA	2193188	NA	0	0	0	0	0	0	0
+NM_213581	chr26	2070404	2084478	-	2034651	NA	2048725	NA	0	0	0	0	0	0	0
+NR_035298	chr26	2086590	2086691	-	2032438	NA	2032539	NA	0	0	0	0	0	0	0
+NR_105470	chr26	2094750	2094860	-	2024269	NA	2024379	NA	0	0	0	0	0	0	0
+NM_001030915	chr26	2117140	2128322	-	1990807	NA	2001989	NA	0	0	0	0	0	0	0
+NM_001031498	chr26	2175178	2177159	-	1941970	NA	1943951	NA	0	0	0	0	0	0	0
+NM_001008452	chr26	2305308	2315138	+	NA	1813821	NA	1803991	0	0	0	0	0	0	0
+NM_001006322	chr26	2315293	2325130	-	1793999	NA	1803836	NA	0	0	0	0	0	0	0
+NM_001004414	chr26	2373245	2375480	-	1743649	NA	1745884	NA	0	0	0	0	0	0	0
+NM_001044644	chr26	2390696	2401255	-	1717874	NA	1728433	NA	0	0	0	0	0	0	0
+NM_001031499	chr26	2425841	2429413	-	1689716	NA	1693288	NA	0	0	0	0	0	0	0
+NM_001033642	chr26	2445710	2453125	+	NA	1673419	NA	1666004	0	0	0	0	0	0	0
+NM_001033643	chr26	2469318	2475028	+	NA	1649811	NA	1644101	0	0	0	0	0	0	0
+NM_204664	chr26	2498398	2509349	+	NA	1620731	NA	1609780	0	0	0	0	0	0	0
+NR_031489	chr26	2511657	2511746	-	1607383	NA	1607472	NA	0	0	0	0	0	0	0
+NR_031490	chr26	2512568	2512648	-	1606481	NA	1606561	NA	0	0	0	0	0	0	0
+NR_105523	chr26	2669792	2669902	-	1449227	NA	1449337	NA	0	0	0	0	0	0	0
+NR_031491	chr26	2896046	2896142	+	NA	1223083	NA	1222987	0	0	0	0	0	0	0
+NM_001190924	chr26	2961382	2962268	+	NA	1157747	NA	1156861	0	0	0	0	0	0	0
+NM_001007881	chr26	2999189	3002725	+	NA	1119940	NA	1116404	0	0	0	0	0	0	0
+NM_204320	chr26	3006741	3011817	-	1107312	NA	1112388	NA	0	0	0	0	0	0	0
+NM_001030916	chr26	3035271	3039335	-	1079794	NA	1083858	NA	0	0	0	0	0	0	0
+NM_204151	chr26	3047964	3050306	-	1068823	NA	1071165	NA	0	0	0	0	0	0	0
+NM_204326	chr26	3124816	3214381	-	904748	NA	994313	NA	0	0	0	0	0	0	0
+NM_204336	chr26	3320769	3332327	+	NA	798360	NA	786802	0	0	0	0	0	0	0
+NM_204622	chr26	3339753	3358863	-	760266	NA	779376	NA	0	0	0	0	0	0	0
+NM_205515	chr26	3359016	3368964	+	NA	760113	NA	750165	0	0	0	0	0	0	0
+NM_001012843	chr26	3370712	3377196	+	NA	748417	NA	741933	0	0	0	0	0	0	0
+NM_001029849	chr26	3377655	3382628	-	736501	NA	741474	NA	0	0	0	0	0	0	0
+NM_001006323	chr26	3439841	3454783	-	664346	NA	679288	NA	0	0	0	0	0	0	0
+NR_035162	chr26	3455233	3455324	+	NA	663896	NA	663805	0	0	0	0	0	0	0
+NM_001012697	chr26	3516478	3545774	+	NA	602651	NA	573355	0	0	0	0	0	0	0
+NM_001030917	chr26	3590932	3597509	-	521620	NA	528197	NA	0	0	0	0	0	0	0
+NM_001031500	chr26	3597231	3600802	+	NA	521898	NA	518327	0	0	0	0	0	0	0
+NM_001040018	chr26	3629575	3631171	+	NA	489554	NA	487958	0	0	0	0	0	0	0
+NM_001257295	chr26	3698350	3701362	-	417767	NA	420779	NA	0	0	0	0	0	0	0
+NM_001257296	chr26	3701377	3715857	-	403272	NA	417752	NA	0	0	0	0	0	0	0
+NM_001012549	chr26	3735643	3742472	-	376657	NA	383486	NA	0	0	0	0	0	0	0
+NM_001030918	chr26	3742618	3760175	-	358954	NA	376511	NA	0	0	0	0	0	0	0
+NM_001006324	chr26	3760758	3765368	-	353761	NA	358371	NA	0	0	0	0	0	0	0
+NM_205063	chr26	3809805	3812700	+	NA	309324	NA	306429	0	0	0	0	0	0	0
+NM_001293109	chr26	3859074	3879130	-	239999	NA	260055	NA	0	0	0	0	0	0	0
+NM_001293108	chr26	3859074	3882051	-	237078	NA	260055	NA	0	0	0	0	0	0	0
+NR_102328	chr26	3916006	3918143	-	200986	NA	203123	NA	0	0	0	0	0	0	0
+NM_204728	chr26	3920817	3937442	-	181687	NA	198312	NA	0	0	0	0	0	0	0
+NM_001244905	chr26	4104910	4108376	+	NA	14219	NA	10753	0	0	0	0	0	0	0
+NM_001293166	chr26	4138324	4142325	-	NA	23196	NA	19195	0	0	0	0	0	0	0
+NM_001030919	chr26	4144091	4175943	+	24962	NA	56814	NA	0	0	0	0	0	0	0
+NM_001257297	chr26	4209891	4216177	+	90762	NA	97048	NA	0	0	0	0	0	0	0
+NM_001257298	chr26	4218028	4238067	+	98899	NA	118938	NA	0	0	0	0	0	0	0
+NM_205490	chr26	4375371	4380959	-	NA	261830	NA	256242	0	0	0	0	0	0	0
+NM_001305129	chr26	4391940	4397490	+	272811	NA	278361	NA	0	0	0	0	0	0	0
+NM_001271612	chr26	4433568	4438784	+	314439	NA	319655	NA	0	0	0	0	0	0	0
+NM_001030920	chr26	4498991	4730550	+	379862	NA	611421	NA	0	0	0	0	0	0	0
+NM_001030921	chr26	4541748	4544997	-	NA	425868	NA	422619	0	0	0	0	0	0	0
+NM_001006325	chr26	4548211	4559974	+	429082	NA	440845	NA	0	0	0	0	0	0	0
+NM_001037832	chr26	4571684	4576072	-	NA	456943	NA	452555	0	0	0	0	0	0	0
+NM_001080870	chr26	4578266	4580646	-	NA	461517	NA	459137	0	0	0	0	0	0	0
+NM_001080868	chr26	4578266	4580647	-	NA	461518	NA	459137	0	0	0	0	0	0	0
+NM_001030922	chr26	4730394	4744364	-	NA	625235	NA	611265	0	0	0	0	0	0	0
+NM_204877	chr26	4751619	4755464	-	NA	636335	NA	632490	0	0	0	0	0	0	0
+NM_001302134	chr26	4791084	4792014	+	671955	NA	672885	NA	0	0	0	0	0	0	0
+NM_001006327	chr26	4828534	4833077	-	NA	713948	NA	709405	0	0	0	0	0	0	0
+NM_001008453	chr26	4838545	4850970	-	NA	731841	NA	719416	0	0	0	0	0	0	0
+NM_001030923	chr26	4876559	4884910	+	757430	NA	765781	NA	0	0	0	0	0	0	0
+NM_204429	chr26	4897094	4901738	-	NA	782609	NA	777965	0	0	0	0	0	0	0
+NM_204967	chr26	4946735	4952662	-	NA	833533	NA	827606	0	0	0	0	0	0	0
+NM_204473	chr26	4990765	4993729	+	871636	NA	874600	NA	0	0	0	0	0	0	0
+NR_105623	chr26	5087926	5087980	-	NA	968851	NA	968797	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out2.log	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,236 @@
+ceas -- 0.9.9.7 (package version 1.0.2)
+INFO  @ Tue, 23 Jun 2015 11:24:09: 
+# ARGUMENTS: 
+# name = ceas
+# gene annotation table = galGal3.refGene
+# BED file = ceas_in.bed
+# WIG file = ceas_in_stp1000.wig
+# extra BED file = None
+# ChIP annotation = On
+# gene-centered annotation =  On
+# average profiling = On
+# dump profiles = Off
+# re-annotation for genome background (ChIP region annotation) = False
+# promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
+# downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
+# bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
+# span size (gene-centered annotation) = 3000 bp
+# profiling resolution (average profiling) = 50 bp
+# relative distance wrt TSS and TTS (average profiling) = 3000 bp 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #1 read the gene table... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #2 read the bed file of ChIP regions... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #3 perform gene-centered annotation... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #4 See ceas.xls for gene-centered annotation! 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #5 read the pre-computed genome bg annotation... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #6 perform ChIP region annotation... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #7 write a R script of ChIP region annotation... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #8-1 run wig profiling of chr26... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #9 append an R script of wig profiling... 
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-redhat-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+  Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # ARGUMENTS: 
+> # name = ceas
+> # gene annotation table = galGal3.refGene
+> # BED file = ceas_in.bed
+> # WIG file = ceas_in_stp1000.wig
+> # extra BED file = None
+> # ChIP annotation = On
+> # gene-centered annotation =  On
+> # average profiling = On
+> # dump profiles = Off
+> # re-annotation for genome background (ChIP region annotation) = False
+> # promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
+> # downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
+> # bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
+> # span size (gene-centered annotation) = 3000 bp
+> # profiling resolution (average profiling) = 50 bp
+> # relative distance wrt TSS and TTS (average profiling) = 3000 bp
+> pdf("ceas.pdf",height=11.5,width=8.5)
+> 
+> # 11:24:09 Tue, 23 Jun 2015
+> # 
+> # ChIP annotation
+> # 
+> 
+> 
+> # 
+> # Chromosomal Distribution
+> # 
+> 
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> r0<-c(100.0)
+> r1<-c(100.0)
+> height<-rbind(r0,r1)
+> names=c("26")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=TRUE,col=c("#5FA1C1","#EB9D86"),main="Chromosomal Distribution of ChIP Regions",xlab="Percentage %",ylab="Chromosome",border=FALSE,xlim=c(0.000000,183.333333),cex.names=1)
+> text(x=c(100.0),y=mp[1,],label=c("100.0 %"),pos=4,offset=0.2,cex=0.9)
+> text(x=c(100.0),y=mp[2,],label=c("100.0 % (<=4.9e-324)"),pos=4,offset=0.2,cex=0.9)
+> legend("right",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> 
+> # 
+> # Promoter,Bipromoter,Downstream, Gene and Regions of interest
+> # 
+> 
+> par(mfrow=c(4, 1),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> r0<-c(1.8532425688606797, 3.616851183410451, 5.322318854623416)
+> r1<-c(0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=1000 bp","<=2000 bp","<=3000 bp")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Promoter",ylab="Percentage %",border=FALSE,ylim=c(0.000000,9.757585),cex.names=1)
+> text(x=mp[1,],y=c(1.8532425688606797, 3.616851183410451, 5.322318854623416),label=c("1.9 %","3.6 %","5.3 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0),label=c("0.000 %
++ (0.981)","0.000 %
++ (0.964)","0.000 %
++ (0.947)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(0.03876062889120376, 0.03876062889120376)
+> r1<-c(0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=2500 bp","<=5000 bp")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Bidirectional Promoter",ylab="Percentage %",border=FALSE,ylim=c(0.000000,0.071061),cex.names=1)
+> text(x=mp[1,],y=c(0.03876062889120376, 0.03876062889120376),label=c("0.04 %","0.04 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0),label=c("0.000 %
++ (1.000)","0.000 %
++ (1.000)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(1.8290171758036773, 3.4690762857627364, 4.980740812519683)
+> r1<-c(0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=1000 bp","<=2000 bp","<=3000 bp")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Downstream",ylab="Percentage %",border=FALSE,ylim=c(0.000000,9.131358),cex.names=1)
+> text(x=mp[1,],y=c(1.8290171758036773, 3.4690762857627364, 4.980740812519683),label=c("1.8 %","3.5 %","5.0 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0),label=c("0.000 %
++ (0.982)","0.000 %
++ (0.965)","0.000 %
++ (0.950)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(0.2034933016788197, 1.3978051793890356, 2.359553283752029, 19.734005184234114, 23.694856949054)
+> r1<-c(0.0, 0.0, 0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("5'UTR","3'UTR","Coding Exon","Intron","All")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Gene",ylab="Percentage %",border=FALSE,ylim=c(0.000000,43.440571),cex.names=1)
+> text(x=mp[1,],y=c(0.2034933016788197, 1.3978051793890356, 2.359553283752029, 19.734005184234114, 23.694856949054),label=c("0.2 %","1.4 %","2.4 %","19.7 %","23.7 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0, 0.0, 0.0),label=c("0.000 %
++ (0.998)","0.000 %
++ (0.986)","0.000 %
++ (0.976)","0.000 %
++ (0.803)","0.000 %
++ (0.763)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> 
+> # 
+> # Distribution of Genome and ChIP regions over cis-regulatory element
+> # Note that the x may be modified for better graphics in case a value is too small
+> # Thus, look at the labels of the pie chart to get the real percentage values
+> # 
+> 
+> par(mfcol=c(2, 2),mar=c(3, 3, 4, 2.8),oma=c(4, 2, 4, 2))
+> x<-c(0.018532,0.017055,0.016037,0.017830,0.015092,0.014051,0.010000,0.013833,0.023014,0.192592,0.670292)
+> pie(x=x,labels=c("1.9 %","1.7 %","1.6 %","1.8 %","1.5 %","1.4 %","0.2 %","1.4 %","2.3 %","19.3 %","67.0 %"),main="Genome",col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),clockwise=TRUE,border=FALSE,radius=0.9,cex=0.8,init.angle=90,density=100)
+> x<-c(0.000000,1.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
+> legend("top",legend=c("Promoter (<=1000 bp): 1.9 %","Promoter (1000-2000 bp): 1.7 %","Promoter (2000-3000 bp): 1.6 %","Downstream (<=1000 bp): 1.8 %","Downstream (1000-2000 bp): 1.5 %","Downstream (2000-3000 bp): 1.4 %","5'UTR: 0.2 %","3'UTR: 1.4 %","Coding exon: 2.3 %","Intron: 19.3 %","Distal intergenic: 67.0 %"),col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),pch=15,bty="n")
+> x<-c(0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,1.000000)
+> pie(x=x,labels=c("0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","100.0 %"),main="ChIP",col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),clockwise=TRUE,border=FALSE,radius=0.9,cex=0.8,init.angle=90,density=100)
+> x<-c(0.000000,1.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
+> legend("top",legend=c("Promoter (<=1000 bp): 0.000 %","Promoter (1000-2000 bp): 0.000 %","Promoter (2000-3000 bp): 0.000 %","Downstream (<=1000 bp): 0.000 %","Downstream (1000-2000 bp): 0.000 %","Downstream (2000-3000 bp): 0.000 %","5'UTR: 0.000 %","3'UTR: 0.000 %","Coding exon: 0.000 %","Intron: 0.000 %","Distal intergenic: 100.0 %"),col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),pch=15,bty="n")
+> 
+> # 
+> # ChIP regions over the genome
+> # 
+> 
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> layout(matrix(c(1, 0, 2, 2), 2, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 5))
+> x<-c(0.000000,0.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="Distribution of Peak Heights",xlab="",ylab="",xlim=c(0.000000,0.000000),ylim=c(0.000000,1.000000),frame=FALSE,xaxt="s",yaxt="n",cex=0.9)
+> x<-c(0.000000,0.000000,0.000000,0.000000)
+> y<-c(0.000000,0.000000,1.000000,1.000000)
+> polygon(x,y,col=c("black"))
+> x <- c(0.000000)
+> y<-c(0.800000)
+> lines(x, y,xlim=c(0, 0.0),ylim=c(0, 1),type="l",col=c("cyan"),lwd=2)
+> x<-c(0.000000,4127518.000000)
+> y<-c(0.855556,1.144444)
+> plot(x, y,type="n",main="ChIP Regions (Peaks) over Chromosomes",xlab="Chromosome Size (bp)",ylab="Chromosome",xlim=c(0.000000,4127518.000000),ylim=c(0.855556,1.144444),frame=FALSE,xaxt="s",yaxt="n")
+> start <- c(4119129)
+> end <- c(4119130)
+> vals <- c(0.0)
+> vals[vals > 0.0] <- 0.0
+> vals[vals < 0] <- 0
+> heights <- 0.288889 * ((vals - 0)/(0.0 - 0)) + 0.855555555556
+> for (i in 1:length(heights)) {
++ 	polygon(x=c(start[i], end[i], end[i], start[i]), y=c(0.855555555556, 0.855555555556, heights[i], heights[i]), col=c("#CC0000"), border=c("#CC0000"))
++ }
+> mtext("26",side=2,line=0,outer=FALSE,at=1.0)
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> layout(matrix(c(1, 2, 3, 3, 4, 5), 3, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 1, 1))
+> x<-c(-3000.000000,-2950.000000,-2900.000000,-2850.000000,-2800.000000,-2750.000000,-2700.000000,-2650.000000,-2600.000000,-2550.000000,-2500.000000,-2450.000000,-2400.000000,-2350.000000,-2300.000000,-2250.000000,-2200.000000,-2150.000000,-2100.000000,-2050.000000,-2000.000000,-1950.000000,-1900.000000,-1850.000000,-1800.000000,-1750.000000,-1700.000000,-1650.000000,-1600.000000,-1550.000000,-1500.000000,-1450.000000,-1400.000000,-1350.000000,-1300.000000,-1250.000000,-1200.000000,-1150.000000,-1100.000000,-1050.000000,-1000.000000,-950.000000,-900.000000,-850.000000,-800.000000,-750.000000,-700.000000,-650.000000,-600.000000,-550.000000,-500.000000,-450.000000,-400.000000,-350.000000,-300.000000,-250.000000,-200.000000,-150.000000,-100.000000,-50.000000,0.000000,50.000000,100.000000,150.000000,200.000000,250.000000,300.000000,350.000000,400.000000,450.000000,500.000000,550.000000,600.000000,650.000000,700.000000,750.000000,800.000000,850.000000,900.000000,950.000000,1000.000000,1050.000000,1100.000000,1150.000000,1200.000000,1250.000000,1300.000000,1350.000000,1400.000000,1450.000000,1500.000000,1550.000000,1600.000000,1650.000000,1700.000000,1750.000000,1800.000000,1850.000000,1900.000000,1950.000000,2000.000000,2050.000000,2100.000000,2150.000000,2200.000000,2250.000000,2300.000000,2350.000000,2400.000000,2450.000000,2500.000000,2550.000000,2600.000000,2650.000000,2700.000000,2750.000000,2800.000000,2850.000000,2900.000000,2950.000000,3000.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Profile near TSS",xlab="Relative Distance to TSS (bp)",ylab="Average Profile",col=c("#C8524D"),xaxt="s",yaxt="s",lwd=2)
+> abline(v=0.000000,lty=2,col=c("black"))
+> x<-c(-3000.000000,-2950.000000,-2900.000000,-2850.000000,-2800.000000,-2750.000000,-2700.000000,-2650.000000,-2600.000000,-2550.000000,-2500.000000,-2450.000000,-2400.000000,-2350.000000,-2300.000000,-2250.000000,-2200.000000,-2150.000000,-2100.000000,-2050.000000,-2000.000000,-1950.000000,-1900.000000,-1850.000000,-1800.000000,-1750.000000,-1700.000000,-1650.000000,-1600.000000,-1550.000000,-1500.000000,-1450.000000,-1400.000000,-1350.000000,-1300.000000,-1250.000000,-1200.000000,-1150.000000,-1100.000000,-1050.000000,-1000.000000,-950.000000,-900.000000,-850.000000,-800.000000,-750.000000,-700.000000,-650.000000,-600.000000,-550.000000,-500.000000,-450.000000,-400.000000,-350.000000,-300.000000,-250.000000,-200.000000,-150.000000,-100.000000,-50.000000,0.000000,50.000000,100.000000,150.000000,200.000000,250.000000,300.000000,350.000000,400.000000,450.000000,500.000000,550.000000,600.000000,650.000000,700.000000,750.000000,800.000000,850.000000,900.000000,950.000000,1000.000000,1050.000000,1100.000000,1150.000000,1200.000000,1250.000000,1300.000000,1350.000000,1400.000000,1450.000000,1500.000000,1550.000000,1600.000000,1650.000000,1700.000000,1750.000000,1800.000000,1850.000000,1900.000000,1950.000000,2000.000000,2050.000000,2100.000000,2150.000000,2200.000000,2250.000000,2300.000000,2350.000000,2400.000000,2450.000000,2500.000000,2550.000000,2600.000000,2650.000000,2700.000000,2750.000000,2800.000000,2850.000000,2900.000000,2950.000000,3000.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Profile near TTS",xlab="Relative Distance to TTS (bp)",ylab="Average Profile",col=c("#C8524D"),xaxt="s",yaxt="s",lwd=2)
+> abline(v=0.000000,lty=2,col=c("black"))
+> x<-c(-1000.000000,-950.000000,-900.000000,-850.000000,-800.000000,-750.000000,-700.000000,-650.000000,-600.000000,-550.000000,-500.000000,-450.000000,-400.000000,-350.000000,-300.000000,-250.000000,-200.000000,-150.000000,-100.000000,-50.000000,0.000000,50.000000,100.000000,150.000000,200.000000,250.000000,300.000000,350.000000,400.000000,450.000000,500.000000,550.000000,600.000000,650.000000,700.000000,750.000000,800.000000,850.000000,900.000000,950.000000,1000.000000,1050.000000,1100.000000,1150.000000,1200.000000,1250.000000,1300.000000,1350.000000,1400.000000,1450.000000,1500.000000,1550.000000,1600.000000,1650.000000,1700.000000,1750.000000,1800.000000,1850.000000,1900.000000,1950.000000,2000.000000,2050.000000,2100.000000,2150.000000,2200.000000,2250.000000,2300.000000,2350.000000,2400.000000,2450.000000,2500.000000,2550.000000,2600.000000,2650.000000,2700.000000,2750.000000,2800.000000,2850.000000,2900.000000,2950.000000,3000.000000,3050.000000,3100.000000,3150.000000,3200.000000,3250.000000,3300.000000,3350.000000,3400.000000,3450.000000,3500.000000,3550.000000,3600.000000,3650.000000,3700.000000,3750.000000,3800.000000,3850.000000,3900.000000,3950.000000,4000.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,238.095238,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Gene Profile",xlab="Upstream (bp), 3000 bp of Meta-gene, Downstream (bp)",ylab="Average Profile",col=c("#C8524D"),xaxt="s",yaxt="s",lwd=2)
+> abline(v=0.000000,lty=2,col=c("black"))
+> abline(v=3000.000000,lty=2,col=c("black"))
+> x<-c(0.000000,3.333333,6.666667,10.000000,13.333333,16.666667,20.000000,23.333333,26.666667,30.000000,33.333333,36.666667,40.000000,43.333333,46.666667,50.000000,53.333333,56.666667,60.000000,63.333333,66.666667,70.000000,73.333333,76.666667,80.000000,83.333333,86.666667,90.000000,93.333333,96.666667,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,250.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Concatenated Exon Profile",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,250.000000),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,3.333333,6.666667,10.000000,13.333333,16.666667,20.000000,23.333333,26.666667,30.000000,33.333333,36.666667,40.000000,43.333333,46.666667,50.000000,53.333333,56.666667,60.000000,63.333333,66.666667,70.000000,73.333333,76.666667,80.000000,83.333333,86.666667,90.000000,93.333333,96.666667,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Concatenated Intron Profile",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,250.000000),xaxt="s",yaxt="s",lwd=2)
+> par(mfrow=c(3, 2),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> x<-c(0.000000,50.000000,100.000000)
+> y<-c(0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Exon Profile
++ (56 <= length < 109 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,25.000000,50.000000,75.000000,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Intron Profile
++ (110 <= length < 345 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,50.000000,100.000000)
+> y<-c(0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Exon Profile
++ (109 <= length < 160 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,11.111111,22.222222,33.333333,44.444444,55.555556,66.666667,77.777778,88.888889,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Intron Profile
++ (344 <= length < 686 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,33.333333,66.666667,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Exon Profile
++ (160 <= length < 375 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,4.761905,9.523810,14.285714,19.047619,23.809524,28.571429,33.333333,38.095238,42.857143,47.619048,52.380952,57.142857,61.904762,66.666667,71.428571,76.190476,80.952381,85.714286,90.476190,95.238095,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,110.497238,0.000000)
+> plot(x, y,type="l",main="Average Intron Profile
++ (685 <= length < 2653 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> dev.off()
+null device 
+          1 
+> 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #... cong! See ceas.pdf for the graphical results of CEAS! 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out2.log.re_match	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,236 @@
+ceas\ \-\-\ 0\.9\.9\.7\ \(package\ version\ 1\.0\.2\)
+INFO\ \ \@\ .* 
+\#\ ARGUMENTS\:\ 
+\#\ name\ \=\ ceas
+\#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
+\#\ BED\ file\ \=\ .*
+\#\ WIG\ file\ \=\ .*
+\#\ extra\ BED\ file\ \=\ None
+\#\ ChIP\ annotation\ \=\ On
+\#\ gene\-centered\ annotation\ \=\ \ On
+\#\ average\ profiling\ \=\ On
+\#\ dump\ profiles\ \=\ Off
+\#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
+\#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
+\#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp
+\#\ profiling\ resolution\ \(average\ profiling\)\ \=\ 50\ bp
+\#\ relative\ distance\ wrt\ TSS\ and\ TTS\ \(average\ profiling\)\ \=\ 3000\ bp\ 
+INFO\ \ \@\ .*\ \#1\ read\ the\ gene\ table\.\.\.\ 
+INFO\ \ \@\ .*\ \#2\ read\ the\ bed\ file\ of\ ChIP\ regions\.\.\.\ 
+INFO\ \ \@\ .*\ \#3\ perform\ gene\-centered\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#4\ See\ ceas\.xls\ for\ gene\-centered\ annotation\!\ 
+INFO\ \ \@\ .*\ \#5\ read\ the\ pre\-computed\ genome\ bg\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#6\ perform\ ChIP\ region\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#7\ write\ a\ R\ script\ of\ ChIP\ region\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#8\-1\ run\ wig\ profiling\ of\ chr26\.\.\.\ 
+INFO\ \ \@\ .*\ \#9\ append\ an\ R\ script\ of\ wig\ profiling\.\.\.\ 
+
+R\ version\ 3\.1\.2\ \(2014\-10\-31\)\ \-\-\ \"Pumpkin\ Helmet\"
+Copyright\ \(C\)\ 2014\ The\ R\ Foundation\ for\ Statistical\ Computing
+Platform\:\ .*
+
+R\ is\ free\ software\ and\ comes\ with\ ABSOLUTELY\ NO\ WARRANTY\.
+You\ are\ welcome\ to\ redistribute\ it\ under\ certain\ conditions\.
+Type\ \'license\(\)\'\ or\ \'licence\(\)\'\ for\ distribution\ details\.
+
+\ \ Natural\ language\ support\ but\ running\ in\ an\ English\ locale
+
+R\ is\ a\ collaborative\ project\ with\ many\ contributors\.
+Type\ \'contributors\(\)\'\ for\ more\ information\ and
+\'citation\(\)\'\ on\ how\ to\ cite\ R\ or\ R\ packages\ in\ publications\.
+
+Type\ \'demo\(\)\'\ for\ some\ demos\,\ \'help\(\)\'\ for\ on\-line\ help\,\ or
+\'help\.start\(\)\'\ for\ an\ HTML\ browser\ interface\ to\ help\.
+Type\ \'q\(\)\'\ to\ quit\ R\.
+
+\>\ \#\ ARGUMENTS\:\ 
+\>\ \#\ name\ \=\ ceas
+\>\ \#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
+\>\ \#\ BED\ file\ \=\ .*
+\>\ \#\ WIG\ file\ \=\ .*
+\>\ \#\ extra\ BED\ file\ \=\ None
+\>\ \#\ ChIP\ annotation\ \=\ On
+\>\ \#\ gene\-centered\ annotation\ \=\ \ On
+\>\ \#\ average\ profiling\ \=\ On
+\>\ \#\ dump\ profiles\ \=\ Off
+\>\ \#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
+\>\ \#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\>\ \#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\>\ \#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
+\>\ \#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp
+\>\ \#\ profiling\ resolution\ \(average\ profiling\)\ \=\ 50\ bp
+\>\ \#\ relative\ distance\ wrt\ TSS\ and\ TTS\ \(average\ profiling\)\ \=\ 3000\ bp
+\>\ pdf\(\"ceas\.pdf\"\,height\=11\.5\,width\=8\.5\)
+\>\ 
+\>\ \#\ .*
+\>\ \#\ 
+\>\ \#\ ChIP\ annotation
+\>\ \#\ 
+\>\ 
+\>\ 
+\>\ \#\ 
+\>\ \#\ Chromosomal\ Distribution
+\>\ \#\ 
+\>\ 
+\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ r0\<\-c\(100\.0\)
+\>\ r1\<\-c\(100\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"26\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=TRUE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Chromosomal\ Distribution\ of\ ChIP\ Regions\"\,xlab\=\"Percentage\ \%\"\,ylab\=\"Chromosome\"\,border\=FALSE\,xlim\=c\(0\.000000\,183\.333333\)\,cex\.names\=1\)
+\>\ text\(x\=c\(100\.0\)\,y\=mp\[1\,\]\,label\=c\(\"100\.0\ \%\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
+\>\ text\(x\=c\(100\.0\)\,y\=mp\[2\,\]\,label\=c\(\"100\.0\ \%\ \(\<\=4\.9e\-324\)\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
+\>\ legend\(\"right\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ 
+\>\ \#\ 
+\>\ \#\ Promoter\,Bipromoter\,Downstream\,\ Gene\ and\ Regions\ of\ interest
+\>\ \#\ 
+\>\ 
+\>\ par\(mfrow\=c\(4\,\ 1\)\,mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ r0\<\-c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.757585\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)\,label\=c\(\"1\.9\ \%\"\,\"3\.6\ \%\"\,\"5\.3\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(0\.981\)\"\,\"0\.000\ \%
+\+\ \(0\.964\)\"\,\"0\.000\ \%
+\+\ \(0\.947\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ r0\<\-c\(0\.03876062889120376\,\ 0\.03876062889120376\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"\<\=2500\ bp\"\,\"\<\=5000\ bp\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Bidirectional\ Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,0\.071061\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(0\.03876062889120376\,\ 0\.03876062889120376\)\,label\=c\(\"0\.04\ \%\"\,\"0\.04\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(1\.000\)\"\,\"0\.000\ \%
+\+\ \(1\.000\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ r0\<\-c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Downstream\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.131358\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)\,label\=c\(\"1\.8\ \%\"\,\"3\.5\ \%\"\,\"5\.0\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(0\.982\)\"\,\"0\.000\ \%
+\+\ \(0\.965\)\"\,\"0\.000\ \%
+\+\ \(0\.950\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ r0\<\-c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"5\'UTR\"\,\"3\'UTR\"\,\"Coding\ Exon\"\,\"Intron\"\,\"All\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Gene\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,43\.440571\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)\,label\=c\(\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.4\ \%\"\,\"19\.7\ \%\"\,\"23\.7\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(0\.998\)\"\,\"0\.000\ \%
+\+\ \(0\.986\)\"\,\"0\.000\ \%
+\+\ \(0\.976\)\"\,\"0\.000\ \%
+\+\ \(0\.803\)\"\,\"0\.000\ \%
+\+\ \(0\.763\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ 
+\>\ \#\ 
+\>\ \#\ Distribution\ of\ Genome\ and\ ChIP\ regions\ over\ cis\-regulatory\ element
+\>\ \#\ Note\ that\ the\ x\ may\ be\ modified\ for\ better\ graphics\ in\ case\ a\ value\ is\ too\ small
+\>\ \#\ Thus\,\ look\ at\ the\ labels\ of\ the\ pie\ chart\ to\ get\ the\ real\ percentage\ values
+\>\ \#\ 
+\>\ 
+\>\ par\(mfcol\=c\(2\,\ 2\)\,mar\=c\(3\,\ 3\,\ 4\,\ 2\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ x\<\-c\(0\.018532\,0\.017055\,0\.016037\,0\.017830\,0\.015092\,0\.014051\,0\.010000\,0\.013833\,0\.023014\,0\.192592\,0\.670292\)
+\>\ pie\(x\=x\,labels\=c\(\"1\.9\ \%\"\,\"1\.7\ \%\"\,\"1\.6\ \%\"\,\"1\.8\ \%\"\,\"1\.5\ \%\"\,\"1\.4\ \%\"\,\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.3\ \%\"\,\"19\.3\ \%\"\,\"67\.0\ \%\"\)\,main\=\"Genome\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
+\>\ x\<\-c\(0\.000000\,1\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 1\.9\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 1\.7\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 1\.6\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 1\.8\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 1\.5\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 1\.4\ \%\"\,\"5\'UTR\:\ 0\.2\ \%\"\,\"3\'UTR\:\ 1\.4\ \%\"\,\"Coding\ exon\:\ 2\.3\ \%\"\,\"Intron\:\ 19\.3\ \%\"\,\"Distal\ intergenic\:\ 67\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ x\<\-c\(0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,1\.000000\)
+\>\ pie\(x\=x\,labels\=c\(\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"100\.0\ \%\"\)\,main\=\"ChIP\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
+\>\ x\<\-c\(0\.000000\,1\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"5\'UTR\:\ 0\.000\ \%\"\,\"3\'UTR\:\ 0\.000\ \%\"\,\"Coding\ exon\:\ 0\.000\ \%\"\,\"Intron\:\ 0\.000\ \%\"\,\"Distal\ intergenic\:\ 100\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ 
+\>\ \#\ 
+\>\ \#\ ChIP\ regions\ over\ the\ genome
+\>\ \#\ 
+\>\ 
+\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ layout\(matrix\(c\(1\,\ 0\,\ 2\,\ 2\)\,\ 2\,\ 2\,\ byrow\ \=\ TRUE\)\,widths\=c\(1\,\ 1\)\,heights\=c\(1\,\ 5\)\)
+\>\ x\<\-c\(0\.000000\,0\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"Distribution\ of\ Peak\ Heights\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(0\.000000\,0\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\,cex\=0\.9\)
+\>\ x\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,1\.000000\,1\.000000\)
+\>\ polygon\(x\,y\,col\=c\(\"black\"\)\)
+\>\ x\ \<\-\ c\(0\.000000\)
+\>\ y\<\-c\(0\.800000\)
+\>\ lines\(x\,\ y\,xlim\=c\(0\,\ 0\.0\)\,ylim\=c\(0\,\ 1\)\,type\=\"l\"\,col\=c\(\"cyan\"\)\,lwd\=2\)
+\>\ x\<\-c\(0\.000000\,4127518\.000000\)
+\>\ y\<\-c\(0\.855556\,1\.144444\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"ChIP\ Regions\ \(Peaks\)\ over\ Chromosomes\"\,xlab\=\"Chromosome\ Size\ \(bp\)\"\,ylab\=\"Chromosome\"\,xlim\=c\(0\.000000\,4127518\.000000\)\,ylim\=c\(0\.855556\,1\.144444\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\)
+\>\ start\ \<\-\ c\(4119129\)
+\>\ end\ \<\-\ c\(4119130\)
+\>\ vals\ \<\-\ c\(0\.0\)
+\>\ vals\[vals\ \>\ 0\.0\]\ \<\-\ 0\.0
+\>\ vals\[vals\ \<\ 0\]\ \<\-\ 0
+\>\ heights\ \<\-\ 0\.288889\ \*\ \(\(vals\ \-\ 0\)\/\(0\.0\ \-\ 0\)\)\ \+\ 0\.855555555556
+\>\ for\ \(i\ in\ 1\:length\(heights\)\)\ \{
+\+\ \	polygon\(x\=c\(start\[i\]\,\ end\[i\]\,\ end\[i\]\,\ start\[i\]\)\,\ y\=c\(0\.855555555556\,\ 0\.855555555556\,\ heights\[i\]\,\ heights\[i\]\)\,\ col\=c\(\"\#CC0000\"\)\,\ border\=c\(\"\#CC0000\"\)\)
+\+\ \}
+\>\ mtext\(\"26\"\,side\=2\,line\=0\,outer\=FALSE\,at\=1\.0\)
+\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ layout\(matrix\(c\(1\,\ 2\,\ 3\,\ 3\,\ 4\,\ 5\)\,\ 3\,\ 2\,\ byrow\ \=\ TRUE\)\,widths\=c\(1\,\ 1\)\,heights\=c\(1\,\ 1\,\ 1\)\)
+\>\ x\<\-c\(\-3000\.000000\,\-2950\.000000\,\-2900\.000000\,\-2850\.000000\,\-2800\.000000\,\-2750\.000000\,\-2700\.000000\,\-2650\.000000\,\-2600\.000000\,\-2550\.000000\,\-2500\.000000\,\-2450\.000000\,\-2400\.000000\,\-2350\.000000\,\-2300\.000000\,\-2250\.000000\,\-2200\.000000\,\-2150\.000000\,\-2100\.000000\,\-2050\.000000\,\-2000\.000000\,\-1950\.000000\,\-1900\.000000\,\-1850\.000000\,\-1800\.000000\,\-1750\.000000\,\-1700\.000000\,\-1650\.000000\,\-1600\.000000\,\-1550\.000000\,\-1500\.000000\,\-1450\.000000\,\-1400\.000000\,\-1350\.000000\,\-1300\.000000\,\-1250\.000000\,\-1200\.000000\,\-1150\.000000\,\-1100\.000000\,\-1050\.000000\,\-1000\.000000\,\-950\.000000\,\-900\.000000\,\-850\.000000\,\-800\.000000\,\-750\.000000\,\-700\.000000\,\-650\.000000\,\-600\.000000\,\-550\.000000\,\-500\.000000\,\-450\.000000\,\-400\.000000\,\-350\.000000\,\-300\.000000\,\-250\.000000\,\-200\.000000\,\-150\.000000\,\-100\.000000\,\-50\.000000\,0\.000000\,50\.000000\,100\.000000\,150\.000000\,200\.000000\,250\.000000\,300\.000000\,350\.000000\,400\.000000\,450\.000000\,500\.000000\,550\.000000\,600\.000000\,650\.000000\,700\.000000\,750\.000000\,800\.000000\,850\.000000\,900\.000000\,950\.000000\,1000\.000000\,1050\.000000\,1100\.000000\,1150\.000000\,1200\.000000\,1250\.000000\,1300\.000000\,1350\.000000\,1400\.000000\,1450\.000000\,1500\.000000\,1550\.000000\,1600\.000000\,1650\.000000\,1700\.000000\,1750\.000000\,1800\.000000\,1850\.000000\,1900\.000000\,1950\.000000\,2000\.000000\,2050\.000000\,2100\.000000\,2150\.000000\,2200\.000000\,2250\.000000\,2300\.000000\,2350\.000000\,2400\.000000\,2450\.000000\,2500\.000000\,2550\.000000\,2600\.000000\,2650\.000000\,2700\.000000\,2750\.000000\,2800\.000000\,2850\.000000\,2900\.000000\,2950\.000000\,3000\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,217\.391304\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Profile\ near\ TSS\"\,xlab\=\"Relative\ Distance\ to\ TSS\ \(bp\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ abline\(v\=0\.000000\,lty\=2\,col\=c\(\"black\"\)\)
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+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Profile\ near\ TTS\"\,xlab\=\"Relative\ Distance\ to\ TTS\ \(bp\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ abline\(v\=0\.000000\,lty\=2\,col\=c\(\"black\"\)\)
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+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Gene\ Profile\"\,xlab\=\"Upstream\ \(bp\)\,\ 3000\ bp\ of\ Meta\-gene\,\ Downstream\ \(bp\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ abline\(v\=0\.000000\,lty\=2\,col\=c\(\"black\"\)\)
+\>\ abline\(v\=3000\.000000\,lty\=2\,col\=c\(\"black\"\)\)
+\>\ x\<\-c\(0\.000000\,3\.333333\,6\.666667\,10\.000000\,13\.333333\,16\.666667\,20\.000000\,23\.333333\,26\.666667\,30\.000000\,33\.333333\,36\.666667\,40\.000000\,43\.333333\,46\.666667\,50\.000000\,53\.333333\,56\.666667\,60\.000000\,63\.333333\,66\.666667\,70\.000000\,73\.333333\,76\.666667\,80\.000000\,83\.333333\,86\.666667\,90\.000000\,93\.333333\,96\.666667\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,250\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Concatenated\ Exon\ Profile\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,250\.000000\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ x\<\-c\(0\.000000\,3\.333333\,6\.666667\,10\.000000\,13\.333333\,16\.666667\,20\.000000\,23\.333333\,26\.666667\,30\.000000\,33\.333333\,36\.666667\,40\.000000\,43\.333333\,46\.666667\,50\.000000\,53\.333333\,56\.666667\,60\.000000\,63\.333333\,66\.666667\,70\.000000\,73\.333333\,76\.666667\,80\.000000\,83\.333333\,86\.666667\,90\.000000\,93\.333333\,96\.666667\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Concatenated\ Intron\ Profile\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,250\.000000\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ par\(mfrow\=c\(3\,\ 2\)\,mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ x\<\-c\(0\.000000\,50\.000000\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Exon\ Profile
+\+\ \(56\ \<\=\ length\ \<\ 109\ bp\)\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,132\.596685\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ x\<\-c\(0\.000000\,25\.000000\,50\.000000\,75\.000000\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Intron\ Profile
+\+\ \(110\ \<\=\ length\ \<\ 345\ bp\)\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,132\.596685\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ x\<\-c\(0\.000000\,50\.000000\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Exon\ Profile
+\+\ \(109\ \<\=\ length\ \<\ 160\ bp\)\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,132\.596685\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ x\<\-c\(0\.000000\,11\.111111\,22\.222222\,33\.333333\,44\.444444\,55\.555556\,66\.666667\,77\.777778\,88\.888889\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Intron\ Profile
+\+\ \(344\ \<\=\ length\ \<\ 686\ bp\)\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,132\.596685\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ x\<\-c\(0\.000000\,33\.333333\,66\.666667\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Exon\ Profile
+\+\ \(160\ \<\=\ length\ \<\ 375\ bp\)\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,132\.596685\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ x\<\-c\(0\.000000\,4\.761905\,9\.523810\,14\.285714\,19\.047619\,23\.809524\,28\.571429\,33\.333333\,38\.095238\,42\.857143\,47\.619048\,52\.380952\,57\.142857\,61\.904762\,66\.666667\,71\.428571\,76\.190476\,80\.952381\,85\.714286\,90\.476190\,95\.238095\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,110\.497238\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Intron\ Profile
+\+\ \(685\ \<\=\ length\ \<\ 2653\ bp\)\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,132\.596685\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ dev\.off\(\)
+null\ device\ 
+\ \ \ \ \ \ \ \ \ \ 1\ 
+\>\ 
+INFO\ \ \@\ .*\ \#\.\.\.\ cong\!\ See\ ceas\.pdf\ for\ the\ graphical\ results\ of\ CEAS\!\ 
Binary file test-data/ceas_out2.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out2.xls	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,133 @@
+# RefSeq: RefSeq ID
+# chr: chromosome of a RefSeq gene
+# txStart: 5' end of a RefSeq gene
+# txEnd: 3' end site of a RefSeq gene
+# strand: strand of a RefSeq gene
+# dist u TSS: Distance to the nearest ChIP region's center upstream of transcription start site (bp)
+# dist d TSS: Distance to the nearest ChIP region's center downstream of transcription start site (bp)
+# dist u TTS: Distance to the nearest ChIP region's center upstream of transcription end site (bp)
+# dist d TTS: Distance to the nearest ChIP region's center downstream of transcription end (bp)
+# 3000bp u TSS: Occupancy rate of ChIP region in 3000bp upstream of transcription start site (0.0 - 1.0)
+# 3000bp d TSS: Occupancy rate of ChIP region in 3000bp downstream of transcription start site (0.0 - 1.0)
+# 1/3 gene: Occupancy rate of ChIP region in 1/3 gene (0.0 - 1.0)
+# 2/3 gene: Occupancy rate of ChIP region in 2/3 gene (0.0 - 1.0)
+# 3/3 gene: Occupancy rate of ChIP region in 3/3 gene (0.0 - 1.0)
+# 3000bp d TTS: Occupancy rate of ChIP region in 3000bp downstream of transcriptino end (0.0 - 1.0)
+# exons: Occupancy rate of ChIP regions in exons (0.0-1.0)
+# Note that txStart and txEnd indicate 5' and 3' ends of genes whereas TSS and TTS transcription start and end sites in consideration of strand.
+#name	chr	txStart	txEnd	strand	dist u TSS	dist d TSS	dist u TTS	dist d TTS	3000bp u TSS	3000bp d TSS	1/3 gene	2/3 gene	3/3 gene	3000bp d TTS	exons
+NM_001031576	chr26	19281	27136	+	NA	4099848	NA	4091993	0	0	0	0	0	0	0
+NM_204615	chr26	57466	61594	-	4057535	NA	4061663	NA	0	0	0	0	0	0	0
+NM_001005431	chr26	65800	76175	-	4042954	NA	4053329	NA	0	0	0	0	0	0	0
+NM_001145491	chr26	91618	92166	-	4026963	NA	4027511	NA	0	0	0	0	0	0	0
+NM_204398	chr26	93069	97423	+	NA	4026060	NA	4021706	0	0	0	0	0	0	0
+NM_001305147	chr26	254661	282571	+	NA	3864468	NA	3836558	0	0	0	0	0	0	0
+NM_001305148	chr26	254661	282571	+	NA	3864468	NA	3836558	0	0	0	0	0	0	0
+NM_001012868	chr26	350397	355252	-	3763877	NA	3768732	NA	0	0	0	0	0	0	0
+NM_001031030	chr26	479573	493561	+	NA	3639556	NA	3625568	0	0	0	0	0	0	0
+NM_001305140	chr26	520705	526012	+	NA	3598424	NA	3593117	0	0	0	0	0	0	0
+NM_001031029	chr26	537101	565572	+	NA	3582028	NA	3553557	0	0	0	0	0	0	0
+NM_205248	chr26	537250	760479	+	NA	3581879	NA	3358650	0	0	0	0	0	0	0
+NM_204727	chr26	662969	683066	-	3436063	NA	3456160	NA	0	0	0	0	0	0	0
+NR_105475	chr26	669012	669122	-	3450007	NA	3450117	NA	0	0	0	0	0	0	0
+NM_205449	chr26	785617	794076	+	NA	3333512	NA	3325053	0	0	0	0	0	0	0
+NM_204681	chr26	897458	902049	-	3217080	NA	3221671	NA	0	0	0	0	0	0	0
+NM_001278156	chr26	905313	917094	-	3202035	NA	3213816	NA	0	0	0	0	0	0	0
+NM_204184	chr26	960209	964268	-	3154861	NA	3158920	NA	0	0	0	0	0	0	0
+NM_204316	chr26	974223	991244	+	NA	3144906	NA	3127885	0	0	0	0	0	0	0
+NM_001031028	chr26	993815	1003847	-	3115282	NA	3125314	NA	0	0	0	0	0	0	0
+NM_001006392	chr26	1024606	1047756	-	3071373	NA	3094523	NA	0	0	0	0	0	0	0
+NM_001039596	chr26	1073550	1080033	-	3039096	NA	3045579	NA	0	0	0	0	0	0	0
+NM_001031027	chr26	1090460	1096137	+	NA	3028669	NA	3022992	0	0	0	0	0	0	0
+NM_001031026	chr26	1096566	1104751	-	3014378	NA	3022563	NA	0	0	0	0	0	0	0
+NM_001030913	chr26	1122296	1132596	+	NA	2996833	NA	2986533	0	0	0	0	0	0	0
+NM_001171886	chr26	1220031	1222791	-	2896338	NA	2899098	NA	0	0	0	0	0	0	0
+NM_205054	chr26	1229703	1232833	+	NA	2889426	NA	2886296	0	0	0	0	0	0	0
+NM_204462	chr26	1234686	1236536	-	2882593	NA	2884443	NA	0	0	0	0	0	0	0
+NM_204463	chr26	1265724	1267989	-	2851140	NA	2853405	NA	0	0	0	0	0	0	0
+NM_001030378	chr26	1289091	1290386	-	2828743	NA	2830038	NA	0	0	0	0	0	0	0
+NM_001195554	chr26	1382510	1388447	+	NA	2736619	NA	2730682	0	0	0	0	0	0	0
+NM_001012548	chr26	1406905	1428443	+	NA	2712224	NA	2690686	0	0	0	0	0	0	0
+NR_031486	chr26	1442696	1442779	-	2676350	NA	2676433	NA	0	0	0	0	0	0	0
+NR_031487	chr26	1442896	1442979	-	2676150	NA	2676233	NA	0	0	0	0	0	0	0
+NM_205250	chr26	1472137	1474003	+	NA	2646992	NA	2645126	0	0	0	0	0	0	0
+NR_105486	chr26	1566398	1566508	-	2552621	NA	2552731	NA	0	0	0	0	0	0	0
+NM_001160320	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001004709	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160324	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001004493	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160323	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160322	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160321	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001004395	chr26	1776431	1800083	+	NA	2342698	NA	2319046	0	0	0	0	0	0	0
+NM_001030914	chr26	1811042	1820368	-	2298761	NA	2308087	NA	0	0	0	0	0	0	0
+NM_204506	chr26	1823407	1843085	-	2276044	NA	2295722	NA	0	0	0	0	0	0	0
+NR_031488	chr26	1925941	1926037	-	2193092	NA	2193188	NA	0	0	0	0	0	0	0
+NM_213581	chr26	2070404	2084478	-	2034651	NA	2048725	NA	0	0	0	0	0	0	0
+NR_035298	chr26	2086590	2086691	-	2032438	NA	2032539	NA	0	0	0	0	0	0	0
+NR_105470	chr26	2094750	2094860	-	2024269	NA	2024379	NA	0	0	0	0	0	0	0
+NM_001030915	chr26	2117140	2128322	-	1990807	NA	2001989	NA	0	0	0	0	0	0	0
+NM_001031498	chr26	2175178	2177159	-	1941970	NA	1943951	NA	0	0	0	0	0	0	0
+NM_001008452	chr26	2305308	2315138	+	NA	1813821	NA	1803991	0	0	0	0	0	0	0
+NM_001006322	chr26	2315293	2325130	-	1793999	NA	1803836	NA	0	0	0	0	0	0	0
+NM_001004414	chr26	2373245	2375480	-	1743649	NA	1745884	NA	0	0	0	0	0	0	0
+NM_001044644	chr26	2390696	2401255	-	1717874	NA	1728433	NA	0	0	0	0	0	0	0
+NM_001031499	chr26	2425841	2429413	-	1689716	NA	1693288	NA	0	0	0	0	0	0	0
+NM_001033642	chr26	2445710	2453125	+	NA	1673419	NA	1666004	0	0	0	0	0	0	0
+NM_001033643	chr26	2469318	2475028	+	NA	1649811	NA	1644101	0	0	0	0	0	0	0
+NM_204664	chr26	2498398	2509349	+	NA	1620731	NA	1609780	0	0	0	0	0	0	0
+NR_031489	chr26	2511657	2511746	-	1607383	NA	1607472	NA	0	0	0	0	0	0	0
+NR_031490	chr26	2512568	2512648	-	1606481	NA	1606561	NA	0	0	0	0	0	0	0
+NR_105523	chr26	2669792	2669902	-	1449227	NA	1449337	NA	0	0	0	0	0	0	0
+NR_031491	chr26	2896046	2896142	+	NA	1223083	NA	1222987	0	0	0	0	0	0	0
+NM_001190924	chr26	2961382	2962268	+	NA	1157747	NA	1156861	0	0	0	0	0	0	0
+NM_001007881	chr26	2999189	3002725	+	NA	1119940	NA	1116404	0	0	0	0	0	0	0
+NM_204320	chr26	3006741	3011817	-	1107312	NA	1112388	NA	0	0	0	0	0	0	0
+NM_001030916	chr26	3035271	3039335	-	1079794	NA	1083858	NA	0	0	0	0	0	0	0
+NM_204151	chr26	3047964	3050306	-	1068823	NA	1071165	NA	0	0	0	0	0	0	0
+NM_204326	chr26	3124816	3214381	-	904748	NA	994313	NA	0	0	0	0	0	0	0
+NM_204336	chr26	3320769	3332327	+	NA	798360	NA	786802	0	0	0	0	0	0	0
+NM_204622	chr26	3339753	3358863	-	760266	NA	779376	NA	0	0	0	0	0	0	0
+NM_205515	chr26	3359016	3368964	+	NA	760113	NA	750165	0	0	0	0	0	0	0
+NM_001012843	chr26	3370712	3377196	+	NA	748417	NA	741933	0	0	0	0	0	0	0
+NM_001029849	chr26	3377655	3382628	-	736501	NA	741474	NA	0	0	0	0	0	0	0
+NM_001006323	chr26	3439841	3454783	-	664346	NA	679288	NA	0	0	0	0	0	0	0
+NR_035162	chr26	3455233	3455324	+	NA	663896	NA	663805	0	0	0	0	0	0	0
+NM_001012697	chr26	3516478	3545774	+	NA	602651	NA	573355	0	0	0	0	0	0	0
+NM_001030917	chr26	3590932	3597509	-	521620	NA	528197	NA	0	0	0	0	0	0	0
+NM_001031500	chr26	3597231	3600802	+	NA	521898	NA	518327	0	0	0	0	0	0	0
+NM_001040018	chr26	3629575	3631171	+	NA	489554	NA	487958	0	0	0	0	0	0	0
+NM_001257295	chr26	3698350	3701362	-	417767	NA	420779	NA	0	0	0	0	0	0	0
+NM_001257296	chr26	3701377	3715857	-	403272	NA	417752	NA	0	0	0	0	0	0	0
+NM_001012549	chr26	3735643	3742472	-	376657	NA	383486	NA	0	0	0	0	0	0	0
+NM_001030918	chr26	3742618	3760175	-	358954	NA	376511	NA	0	0	0	0	0	0	0
+NM_001006324	chr26	3760758	3765368	-	353761	NA	358371	NA	0	0	0	0	0	0	0
+NM_205063	chr26	3809805	3812700	+	NA	309324	NA	306429	0	0	0	0	0	0	0
+NM_001293109	chr26	3859074	3879130	-	239999	NA	260055	NA	0	0	0	0	0	0	0
+NM_001293108	chr26	3859074	3882051	-	237078	NA	260055	NA	0	0	0	0	0	0	0
+NR_102328	chr26	3916006	3918143	-	200986	NA	203123	NA	0	0	0	0	0	0	0
+NM_204728	chr26	3920817	3937442	-	181687	NA	198312	NA	0	0	0	0	0	0	0
+NM_001244905	chr26	4104910	4108376	+	NA	14219	NA	10753	0	0	0	0	0	0	0
+NM_001293166	chr26	4138324	4142325	-	NA	23196	NA	19195	0	0	0	0	0	0	0
+NM_001030919	chr26	4144091	4175943	+	24962	NA	56814	NA	0	0	0	0	0	0	0
+NM_001257297	chr26	4209891	4216177	+	90762	NA	97048	NA	0	0	0	0	0	0	0
+NM_001257298	chr26	4218028	4238067	+	98899	NA	118938	NA	0	0	0	0	0	0	0
+NM_205490	chr26	4375371	4380959	-	NA	261830	NA	256242	0	0	0	0	0	0	0
+NM_001305129	chr26	4391940	4397490	+	272811	NA	278361	NA	0	0	0	0	0	0	0
+NM_001271612	chr26	4433568	4438784	+	314439	NA	319655	NA	0	0	0	0	0	0	0
+NM_001030920	chr26	4498991	4730550	+	379862	NA	611421	NA	0	0	0	0	0	0	0
+NM_001030921	chr26	4541748	4544997	-	NA	425868	NA	422619	0	0	0	0	0	0	0
+NM_001006325	chr26	4548211	4559974	+	429082	NA	440845	NA	0	0	0	0	0	0	0
+NM_001037832	chr26	4571684	4576072	-	NA	456943	NA	452555	0	0	0	0	0	0	0
+NM_001080870	chr26	4578266	4580646	-	NA	461517	NA	459137	0	0	0	0	0	0	0
+NM_001080868	chr26	4578266	4580647	-	NA	461518	NA	459137	0	0	0	0	0	0	0
+NM_001030922	chr26	4730394	4744364	-	NA	625235	NA	611265	0	0	0	0	0	0	0
+NM_204877	chr26	4751619	4755464	-	NA	636335	NA	632490	0	0	0	0	0	0	0
+NM_001302134	chr26	4791084	4792014	+	671955	NA	672885	NA	0	0	0	0	0	0	0
+NM_001006327	chr26	4828534	4833077	-	NA	713948	NA	709405	0	0	0	0	0	0	0
+NM_001008453	chr26	4838545	4850970	-	NA	731841	NA	719416	0	0	0	0	0	0	0
+NM_001030923	chr26	4876559	4884910	+	757430	NA	765781	NA	0	0	0	0	0	0	0
+NM_204429	chr26	4897094	4901738	-	NA	782609	NA	777965	0	0	0	0	0	0	0
+NM_204967	chr26	4946735	4952662	-	NA	833533	NA	827606	0	0	0	0	0	0	0
+NM_204473	chr26	4990765	4993729	+	871636	NA	874600	NA	0	0	0	0	0	0	0
+NR_105623	chr26	5087926	5087980	-	NA	968851	NA	968797	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out3.log	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,235 @@
+/home/pjb/galaxy-tools/ceas/test.tool_dependencies.ceas/bx_python/0.7.1/lib/python2.7/site-packages/pkg_resources.py:1054: UserWarning: /home/pjb/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
+  warnings.warn(msg, UserWarning)
+ceasBW -- 0.9.9.7 (package version 1.0.2)
+/home/pjb/galaxy-tools/ceas/test.tool_dependencies.ceas/bx_python/0.7.1/lib/python2.7/site-packages/pkg_resources.py:1054: UserWarning: /home/pjb/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
+  warnings.warn(msg, UserWarning)
+INFO  @ Tue, 23 Jun 2015 13:03:32: 
+# ARGUMENTS: 
+# name = ceas
+# gene annotation table = galGal3.refGene
+# BED file = ceas_in.bed
+# WIG file = ceas_in.bigwig
+# extra BED file = None
+# ChIP annotation = On
+# gene-centered annotation =  On
+# average profiling = On
+# dump profiles = Off
+# re-annotation for genome background (ChIP region annotation) = False
+# promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
+# downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
+# bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
+# span size (gene-centered annotation) = 3000 bp
+# profiling resolution (average profiling) = 50 bp
+# relative distance wrt TSS and TTS (average profiling) = 3000 bp 
+INFO  @ Tue, 23 Jun 2015 13:03:32: #1 read the gene table... 
+INFO  @ Tue, 23 Jun 2015 13:03:32: #2 read the bed file of ChIP regions... 
+INFO  @ Tue, 23 Jun 2015 13:03:32: #3 perform gene-centered annotation... 
+INFO  @ Tue, 23 Jun 2015 13:03:32: #4 See ceas.xls for gene-centered annotation! 
+INFO  @ Tue, 23 Jun 2015 13:03:32: #5 read the pre-computed genome bg annotation... 
+INFO  @ Tue, 23 Jun 2015 13:03:32: #6 perform ChIP region annotation... 
+INFO  @ Tue, 23 Jun 2015 13:03:32: #7 write a R script of ChIP region annotation... 
+INFO  @ Tue, 23 Jun 2015 13:03:32: #8-1 run wig profiling of chr26... 
+INFO  @ Tue, 23 Jun 2015 13:03:32: #9 append an R script of wig profiling... 
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-redhat-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+  Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # ARGUMENTS: 
+> # name = ceas
+> # gene annotation table = galGal3.refGene
+> # BED file = ceas_in.bed
+> # WIG file = ceas_in.bigwig
+> # extra BED file = None
+> # ChIP annotation = On
+> # gene-centered annotation =  On
+> # average profiling = On
+> # dump profiles = Off
+> # re-annotation for genome background (ChIP region annotation) = False
+> # promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
+> # downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
+> # bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
+> # span size (gene-centered annotation) = 3000 bp
+> # profiling resolution (average profiling) = 50 bp
+> # relative distance wrt TSS and TTS (average profiling) = 3000 bp
+> pdf("ceas.pdf",height=11.5,width=8.5)
+> 
+> # 13:03:32 Tue, 23 Jun 2015
+> # 
+> # ChIP annotation
+> # 
+> 
+> 
+> # 
+> # Chromosomal Distribution
+> # 
+> 
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> r0<-c(100.0)
+> r1<-c(100.0)
+> height<-rbind(r0,r1)
+> names=c("26")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=TRUE,col=c("#5FA1C1","#EB9D86"),main="Chromosomal Distribution of ChIP Regions",xlab="Percentage %",ylab="Chromosome",border=FALSE,xlim=c(0.000000,183.333333),cex.names=1)
+> text(x=c(100.0),y=mp[1,],label=c("100.0 %"),pos=4,offset=0.2,cex=0.9)
+> text(x=c(100.0),y=mp[2,],label=c("100.0 % (<=4.9e-324)"),pos=4,offset=0.2,cex=0.9)
+> legend("right",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> 
+> # 
+> # Promoter,Bipromoter,Downstream, Gene and Regions of interest
+> # 
+> 
+> par(mfrow=c(4, 1),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> r0<-c(1.8532425688606797, 3.616851183410451, 5.322318854623416)
+> r1<-c(0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=1000 bp","<=2000 bp","<=3000 bp")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Promoter",ylab="Percentage %",border=FALSE,ylim=c(0.000000,9.757585),cex.names=1)
+> text(x=mp[1,],y=c(1.8532425688606797, 3.616851183410451, 5.322318854623416),label=c("1.9 %","3.6 %","5.3 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0),label=c("0.000 %
++ (0.981)","0.000 %
++ (0.964)","0.000 %
++ (0.947)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(0.03876062889120376, 0.03876062889120376)
+> r1<-c(0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=2500 bp","<=5000 bp")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Bidirectional Promoter",ylab="Percentage %",border=FALSE,ylim=c(0.000000,0.071061),cex.names=1)
+> text(x=mp[1,],y=c(0.03876062889120376, 0.03876062889120376),label=c("0.04 %","0.04 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0),label=c("0.000 %
++ (1.000)","0.000 %
++ (1.000)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(1.8290171758036773, 3.4690762857627364, 4.980740812519683)
+> r1<-c(0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=1000 bp","<=2000 bp","<=3000 bp")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Downstream",ylab="Percentage %",border=FALSE,ylim=c(0.000000,9.131358),cex.names=1)
+> text(x=mp[1,],y=c(1.8290171758036773, 3.4690762857627364, 4.980740812519683),label=c("1.8 %","3.5 %","5.0 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0),label=c("0.000 %
++ (0.982)","0.000 %
++ (0.965)","0.000 %
++ (0.950)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(0.2034933016788197, 1.3978051793890356, 2.359553283752029, 19.734005184234114, 23.694856949054)
+> r1<-c(0.0, 0.0, 0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("5'UTR","3'UTR","Coding Exon","Intron","All")
+> mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Gene",ylab="Percentage %",border=FALSE,ylim=c(0.000000,43.440571),cex.names=1)
+> text(x=mp[1,],y=c(0.2034933016788197, 1.3978051793890356, 2.359553283752029, 19.734005184234114, 23.694856949054),label=c("0.2 %","1.4 %","2.4 %","19.7 %","23.7 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0, 0.0, 0.0),label=c("0.000 %
++ (0.998)","0.000 %
++ (0.986)","0.000 %
++ (0.976)","0.000 %
++ (0.803)","0.000 %
++ (0.763)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> 
+> # 
+> # Distribution of Genome and ChIP regions over cis-regulatory element
+> # Note that the x may be modified for better graphics in case a value is too small
+> # Thus, look at the labels of the pie chart to get the real percentage values
+> # 
+> 
+> par(mfcol=c(2, 2),mar=c(3, 3, 4, 2.8),oma=c(4, 2, 4, 2))
+> x<-c(0.018532,0.017055,0.016037,0.017830,0.015092,0.014051,0.010000,0.013833,0.023014,0.192592,0.670292)
+> pie(x=x,labels=c("1.9 %","1.7 %","1.6 %","1.8 %","1.5 %","1.4 %","0.2 %","1.4 %","2.3 %","19.3 %","67.0 %"),main="Genome",col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),clockwise=TRUE,border=FALSE,radius=0.9,cex=0.8,init.angle=90,density=100)
+> x<-c(0.000000,1.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
+> legend("top",legend=c("Promoter (<=1000 bp): 1.9 %","Promoter (1000-2000 bp): 1.7 %","Promoter (2000-3000 bp): 1.6 %","Downstream (<=1000 bp): 1.8 %","Downstream (1000-2000 bp): 1.5 %","Downstream (2000-3000 bp): 1.4 %","5'UTR: 0.2 %","3'UTR: 1.4 %","Coding exon: 2.3 %","Intron: 19.3 %","Distal intergenic: 67.0 %"),col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),pch=15,bty="n")
+> x<-c(0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,1.000000)
+> pie(x=x,labels=c("0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","0.000 %","100.0 %"),main="ChIP",col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),clockwise=TRUE,border=FALSE,radius=0.9,cex=0.8,init.angle=90,density=100)
+> x<-c(0.000000,1.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
+> legend("top",legend=c("Promoter (<=1000 bp): 0.000 %","Promoter (1000-2000 bp): 0.000 %","Promoter (2000-3000 bp): 0.000 %","Downstream (<=1000 bp): 0.000 %","Downstream (1000-2000 bp): 0.000 %","Downstream (2000-3000 bp): 0.000 %","5'UTR: 0.000 %","3'UTR: 0.000 %","Coding exon: 0.000 %","Intron: 0.000 %","Distal intergenic: 100.0 %"),col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),pch=15,bty="n")
+> 
+> # 
+> # ChIP regions over the genome
+> # 
+> 
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> layout(matrix(c(1, 0, 2, 2), 2, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 5))
+> x<-c(0.000000,0.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="Distribution of Peak Heights",xlab="",ylab="",xlim=c(0.000000,0.000000),ylim=c(0.000000,1.000000),frame=FALSE,xaxt="s",yaxt="n",cex=0.9)
+> x<-c(0.000000,0.000000,0.000000,0.000000)
+> y<-c(0.000000,0.000000,1.000000,1.000000)
+> polygon(x,y,col=c("black"))
+> x <- c(0.000000)
+> y<-c(0.800000)
+> lines(x, y,xlim=c(0, 0.0),ylim=c(0, 1),type="l",col=c("cyan"),lwd=2)
+> x<-c(0.000000,4127518.000000)
+> y<-c(0.855556,1.144444)
+> plot(x, y,type="n",main="ChIP Regions (Peaks) over Chromosomes",xlab="Chromosome Size (bp)",ylab="Chromosome",xlim=c(0.000000,4127518.000000),ylim=c(0.855556,1.144444),frame=FALSE,xaxt="s",yaxt="n")
+> start <- c(4119129)
+> end <- c(4119130)
+> vals <- c(0.0)
+> vals[vals > 0.0] <- 0.0
+> vals[vals < 0] <- 0
+> heights <- 0.288889 * ((vals - 0)/(0.0 - 0)) + 0.855555555556
+> for (i in 1:length(heights)) {
++ 	polygon(x=c(start[i], end[i], end[i], start[i]), y=c(0.855555555556, 0.855555555556, heights[i], heights[i]), col=c("#CC0000"), border=c("#CC0000"))
++ }
+> mtext("26",side=2,line=0,outer=FALSE,at=1.0)
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> layout(matrix(c(1, 2, 3, 3, 4, 5), 3, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 1, 1))
+> x<-c(-3000.000000,-2950.000000,-2900.000000,-2850.000000,-2800.000000,-2750.000000,-2700.000000,-2650.000000,-2600.000000,-2550.000000,-2500.000000,-2450.000000,-2400.000000,-2350.000000,-2300.000000,-2250.000000,-2200.000000,-2150.000000,-2100.000000,-2050.000000,-2000.000000,-1950.000000,-1900.000000,-1850.000000,-1800.000000,-1750.000000,-1700.000000,-1650.000000,-1600.000000,-1550.000000,-1500.000000,-1450.000000,-1400.000000,-1350.000000,-1300.000000,-1250.000000,-1200.000000,-1150.000000,-1100.000000,-1050.000000,-1000.000000,-950.000000,-900.000000,-850.000000,-800.000000,-750.000000,-700.000000,-650.000000,-600.000000,-550.000000,-500.000000,-450.000000,-400.000000,-350.000000,-300.000000,-250.000000,-200.000000,-150.000000,-100.000000,-50.000000,0.000000,50.000000,100.000000,150.000000,200.000000,250.000000,300.000000,350.000000,400.000000,450.000000,500.000000,550.000000,600.000000,650.000000,700.000000,750.000000,800.000000,850.000000,900.000000,950.000000,1000.000000,1050.000000,1100.000000,1150.000000,1200.000000,1250.000000,1300.000000,1350.000000,1400.000000,1450.000000,1500.000000,1550.000000,1600.000000,1650.000000,1700.000000,1750.000000,1800.000000,1850.000000,1900.000000,1950.000000,2000.000000,2050.000000,2100.000000,2150.000000,2200.000000,2250.000000,2300.000000,2350.000000,2400.000000,2450.000000,2500.000000,2550.000000,2600.000000,2650.000000,2700.000000,2750.000000,2800.000000,2850.000000,2900.000000,2950.000000,3000.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Profile near TSS",xlab="Relative Distance to TSS (bp)",ylab="Average Profile",col=c("#C8524D"),xaxt="s",yaxt="s",lwd=2)
+> abline(v=0.000000,lty=2,col=c("black"))
+> x<-c(-3000.000000,-2950.000000,-2900.000000,-2850.000000,-2800.000000,-2750.000000,-2700.000000,-2650.000000,-2600.000000,-2550.000000,-2500.000000,-2450.000000,-2400.000000,-2350.000000,-2300.000000,-2250.000000,-2200.000000,-2150.000000,-2100.000000,-2050.000000,-2000.000000,-1950.000000,-1900.000000,-1850.000000,-1800.000000,-1750.000000,-1700.000000,-1650.000000,-1600.000000,-1550.000000,-1500.000000,-1450.000000,-1400.000000,-1350.000000,-1300.000000,-1250.000000,-1200.000000,-1150.000000,-1100.000000,-1050.000000,-1000.000000,-950.000000,-900.000000,-850.000000,-800.000000,-750.000000,-700.000000,-650.000000,-600.000000,-550.000000,-500.000000,-450.000000,-400.000000,-350.000000,-300.000000,-250.000000,-200.000000,-150.000000,-100.000000,-50.000000,0.000000,50.000000,100.000000,150.000000,200.000000,250.000000,300.000000,350.000000,400.000000,450.000000,500.000000,550.000000,600.000000,650.000000,700.000000,750.000000,800.000000,850.000000,900.000000,950.000000,1000.000000,1050.000000,1100.000000,1150.000000,1200.000000,1250.000000,1300.000000,1350.000000,1400.000000,1450.000000,1500.000000,1550.000000,1600.000000,1650.000000,1700.000000,1750.000000,1800.000000,1850.000000,1900.000000,1950.000000,2000.000000,2050.000000,2100.000000,2150.000000,2200.000000,2250.000000,2300.000000,2350.000000,2400.000000,2450.000000,2500.000000,2550.000000,2600.000000,2650.000000,2700.000000,2750.000000,2800.000000,2850.000000,2900.000000,2950.000000,3000.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Profile near TTS",xlab="Relative Distance to TTS (bp)",ylab="Average Profile",col=c("#C8524D"),xaxt="s",yaxt="s",lwd=2)
+> abline(v=0.000000,lty=2,col=c("black"))
+> x<-c(-1000.000000,-950.000000,-900.000000,-850.000000,-800.000000,-750.000000,-700.000000,-650.000000,-600.000000,-550.000000,-500.000000,-450.000000,-400.000000,-350.000000,-300.000000,-250.000000,-200.000000,-150.000000,-100.000000,-50.000000,0.000000,50.000000,100.000000,150.000000,200.000000,250.000000,300.000000,350.000000,400.000000,450.000000,500.000000,550.000000,600.000000,650.000000,700.000000,750.000000,800.000000,850.000000,900.000000,950.000000,1000.000000,1050.000000,1100.000000,1150.000000,1200.000000,1250.000000,1300.000000,1350.000000,1400.000000,1450.000000,1500.000000,1550.000000,1600.000000,1650.000000,1700.000000,1750.000000,1800.000000,1850.000000,1900.000000,1950.000000,2000.000000,2050.000000,2100.000000,2150.000000,2200.000000,2250.000000,2300.000000,2350.000000,2400.000000,2450.000000,2500.000000,2550.000000,2600.000000,2650.000000,2700.000000,2750.000000,2800.000000,2850.000000,2900.000000,2950.000000,3000.000000,3050.000000,3100.000000,3150.000000,3200.000000,3250.000000,3300.000000,3350.000000,3400.000000,3450.000000,3500.000000,3550.000000,3600.000000,3650.000000,3700.000000,3750.000000,3800.000000,3850.000000,3900.000000,3950.000000,4000.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Gene Profile",xlab="Upstream (bp), 3000 bp of Meta-gene, Downstream (bp)",ylab="Average Profile",col=c("#C8524D"),xaxt="s",yaxt="s",lwd=2)
+> abline(v=0.000000,lty=2,col=c("black"))
+> abline(v=3000.000000,lty=2,col=c("black"))
+> x<-c(0.000000,3.333333,6.666667,10.000000,13.333333,16.666667,20.000000,23.333333,26.666667,30.000000,33.333333,36.666667,40.000000,43.333333,46.666667,50.000000,53.333333,56.666667,60.000000,63.333333,66.666667,70.000000,73.333333,76.666667,80.000000,83.333333,86.666667,90.000000,93.333333,96.666667,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Concatenated Exon Profile",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,20000.000000),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,3.333333,6.666667,10.000000,13.333333,16.666667,20.000000,23.333333,26.666667,30.000000,33.333333,36.666667,40.000000,43.333333,46.666667,50.000000,53.333333,56.666667,60.000000,63.333333,66.666667,70.000000,73.333333,76.666667,80.000000,83.333333,86.666667,90.000000,93.333333,96.666667,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Concatenated Intron Profile",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,20000.000000),xaxt="s",yaxt="s",lwd=2)
+> par(mfrow=c(3, 2),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> x<-c(-3.000000,3.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",xlim=c(-3.000000,3.000000),ylim=c(0.000000,1.000000),axes=FALSE,xaxt="s",yaxt="s")
+> x<-c(-3.000000,3.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",xlim=c(-3.000000,3.000000),ylim=c(0.000000,1.000000),axes=FALSE,xaxt="s",yaxt="s")
+> x<-c(-3.000000,3.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",xlim=c(-3.000000,3.000000),ylim=c(0.000000,1.000000),axes=FALSE,xaxt="s",yaxt="s")
+> x<-c(-3.000000,3.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",xlim=c(-3.000000,3.000000),ylim=c(0.000000,1.000000),axes=FALSE,xaxt="s",yaxt="s")
+> x<-c(-3.000000,3.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",xlim=c(-3.000000,3.000000),ylim=c(0.000000,1.000000),axes=FALSE,xaxt="s",yaxt="s")
+> x<-c(0.000000,4.761905,9.523810,14.285714,19.047619,23.809524,28.571429,33.333333,38.095238,42.857143,47.619048,52.380952,57.142857,61.904762,66.666667,71.428571,76.190476,80.952381,85.714286,90.476190,95.238095,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,20000.000000,0.000000)
+> plot(x, y,type="l",main="Average Intron Profile
++ (685 <= length < 2653 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,24000.000000),xaxt="s",yaxt="s",lwd=2)
+> dev.off()
+null device 
+          1 
+> 
+INFO  @ Tue, 23 Jun 2015 13:03:33: #... cong! See ceas.pdf for the graphical results of CEAS! 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out3.log.re_match	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,231 @@
+ceasBW\ \-\-\ 0\.9\.9\.7\ \(package\ version\ 1\.0\.2\)
+INFO\ \ \@\ .*\ 
+\#\ ARGUMENTS\:\ 
+\#\ name\ \=\ ceas
+\#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
+\#\ BED\ file\ \=\ .*
+\#\ WIG\ file\ \=\ .*
+\#\ extra\ BED\ file\ \=\ None
+\#\ ChIP\ annotation\ \=\ On
+\#\ gene\-centered\ annotation\ \=\ \ On
+\#\ average\ profiling\ \=\ On
+\#\ dump\ profiles\ \=\ Off
+\#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
+\#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
+\#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp
+\#\ profiling\ resolution\ \(average\ profiling\)\ \=\ 50\ bp
+\#\ relative\ distance\ wrt\ TSS\ and\ TTS\ \(average\ profiling\)\ \=\ 3000\ bp\ 
+INFO\ \ \@\ .*\ \#1\ read\ the\ gene\ table\.\.\.\ 
+INFO\ \ \@\ .*\ \#2\ read\ the\ bed\ file\ of\ ChIP\ regions\.\.\.\ 
+INFO\ \ \@\ .*\ \#3\ perform\ gene\-centered\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#4\ See\ ceas\.xls\ for\ gene\-centered\ annotation\!\ 
+INFO\ \ \@\ .*\ \#5\ read\ the\ pre\-computed\ genome\ bg\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#6\ perform\ ChIP\ region\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#7\ write\ a\ R\ script\ of\ ChIP\ region\ annotation\.\.\.\ 
+INFO\ \ \@\ .*\ \#8\-1\ run\ wig\ profiling\ of\ chr26\.\.\.\ 
+INFO\ \ \@\ .*\ \#9\ append\ an\ R\ script\ of\ wig\ profiling\.\.\.\ 
+
+R\ version\ 3\.1\.2\ \(2014\-10\-31\)\ \-\-\ \"Pumpkin\ Helmet\"
+Copyright\ \(C\)\ 2014\ The\ R\ Foundation\ for\ Statistical\ Computing
+Platform\:\ .*
+
+R\ is\ free\ software\ and\ comes\ with\ ABSOLUTELY\ NO\ WARRANTY\.
+You\ are\ welcome\ to\ redistribute\ it\ under\ certain\ conditions\.
+Type\ \'license\(\)\'\ or\ \'licence\(\)\'\ for\ distribution\ details\.
+
+\ \ Natural\ language\ support\ but\ running\ in\ an\ English\ locale
+
+R\ is\ a\ collaborative\ project\ with\ many\ contributors\.
+Type\ \'contributors\(\)\'\ for\ more\ information\ and
+\'citation\(\)\'\ on\ how\ to\ cite\ R\ or\ R\ packages\ in\ publications\.
+
+Type\ \'demo\(\)\'\ for\ some\ demos\,\ \'help\(\)\'\ for\ on\-line\ help\,\ or
+\'help\.start\(\)\'\ for\ an\ HTML\ browser\ interface\ to\ help\.
+Type\ \'q\(\)\'\ to\ quit\ R\.
+
+\>\ \#\ ARGUMENTS\:\ 
+\>\ \#\ name\ \=\ ceas
+\>\ \#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
+\>\ \#\ BED\ file\ \=\ .*
+\>\ \#\ WIG\ file\ \=\ .*
+\>\ \#\ extra\ BED\ file\ \=\ None
+\>\ \#\ ChIP\ annotation\ \=\ On
+\>\ \#\ gene\-centered\ annotation\ \=\ \ On
+\>\ \#\ average\ profiling\ \=\ On
+\>\ \#\ dump\ profiles\ \=\ Off
+\>\ \#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
+\>\ \#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\>\ \#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
+\>\ \#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
+\>\ \#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp
+\>\ \#\ profiling\ resolution\ \(average\ profiling\)\ \=\ 50\ bp
+\>\ \#\ relative\ distance\ wrt\ TSS\ and\ TTS\ \(average\ profiling\)\ \=\ 3000\ bp
+\>\ pdf\(\"ceas\.pdf\"\,height\=11\.5\,width\=8\.5\)
+\>\ 
+\>\ \#\ .*
+\>\ \#\ 
+\>\ \#\ ChIP\ annotation
+\>\ \#\ 
+\>\ 
+\>\ 
+\>\ \#\ 
+\>\ \#\ Chromosomal\ Distribution
+\>\ \#\ 
+\>\ 
+\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ r0\<\-c\(100\.0\)
+\>\ r1\<\-c\(100\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"26\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=TRUE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Chromosomal\ Distribution\ of\ ChIP\ Regions\"\,xlab\=\"Percentage\ \%\"\,ylab\=\"Chromosome\"\,border\=FALSE\,xlim\=c\(0\.000000\,183\.333333\)\,cex\.names\=1\)
+\>\ text\(x\=c\(100\.0\)\,y\=mp\[1\,\]\,label\=c\(\"100\.0\ \%\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
+\>\ text\(x\=c\(100\.0\)\,y\=mp\[2\,\]\,label\=c\(\"100\.0\ \%\ \(\<\=4\.9e\-324\)\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
+\>\ legend\(\"right\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ 
+\>\ \#\ 
+\>\ \#\ Promoter\,Bipromoter\,Downstream\,\ Gene\ and\ Regions\ of\ interest
+\>\ \#\ 
+\>\ 
+\>\ par\(mfrow\=c\(4\,\ 1\)\,mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ r0\<\-c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.757585\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)\,label\=c\(\"1\.9\ \%\"\,\"3\.6\ \%\"\,\"5\.3\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(0\.981\)\"\,\"0\.000\ \%
+\+\ \(0\.964\)\"\,\"0\.000\ \%
+\+\ \(0\.947\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ r0\<\-c\(0\.03876062889120376\,\ 0\.03876062889120376\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"\<\=2500\ bp\"\,\"\<\=5000\ bp\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Bidirectional\ Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,0\.071061\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(0\.03876062889120376\,\ 0\.03876062889120376\)\,label\=c\(\"0\.04\ \%\"\,\"0\.04\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(1\.000\)\"\,\"0\.000\ \%
+\+\ \(1\.000\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ r0\<\-c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Downstream\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.131358\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)\,label\=c\(\"1\.8\ \%\"\,\"3\.5\ \%\"\,\"5\.0\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(0\.982\)\"\,\"0\.000\ \%
+\+\ \(0\.965\)\"\,\"0\.000\ \%
+\+\ \(0\.950\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ r0\<\-c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)
+\>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)
+\>\ height\<\-rbind\(r0\,r1\)
+\>\ names\=c\(\"5\'UTR\"\,\"3\'UTR\"\,\"Coding\ Exon\"\,\"Intron\"\,\"All\"\)
+\>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Gene\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,43\.440571\)\,cex\.names\=1\)
+\>\ text\(x\=mp\[1\,\]\,y\=c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)\,label\=c\(\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.4\ \%\"\,\"19\.7\ \%\"\,\"23\.7\ \%\"\)\,pos\=3\,offset\=0\.2\)
+\>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
+\+\ \(0\.998\)\"\,\"0\.000\ \%
+\+\ \(0\.986\)\"\,\"0\.000\ \%
+\+\ \(0\.976\)\"\,\"0\.000\ \%
+\+\ \(0\.803\)\"\,\"0\.000\ \%
+\+\ \(0\.763\)\"\)\,pos\=3\,offset\=0\.2\)
+\>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ 
+\>\ \#\ 
+\>\ \#\ Distribution\ of\ Genome\ and\ ChIP\ regions\ over\ cis\-regulatory\ element
+\>\ \#\ Note\ that\ the\ x\ may\ be\ modified\ for\ better\ graphics\ in\ case\ a\ value\ is\ too\ small
+\>\ \#\ Thus\,\ look\ at\ the\ labels\ of\ the\ pie\ chart\ to\ get\ the\ real\ percentage\ values
+\>\ \#\ 
+\>\ 
+\>\ par\(mfcol\=c\(2\,\ 2\)\,mar\=c\(3\,\ 3\,\ 4\,\ 2\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ x\<\-c\(0\.018532\,0\.017055\,0\.016037\,0\.017830\,0\.015092\,0\.014051\,0\.010000\,0\.013833\,0\.023014\,0\.192592\,0\.670292\)
+\>\ pie\(x\=x\,labels\=c\(\"1\.9\ \%\"\,\"1\.7\ \%\"\,\"1\.6\ \%\"\,\"1\.8\ \%\"\,\"1\.5\ \%\"\,\"1\.4\ \%\"\,\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.3\ \%\"\,\"19\.3\ \%\"\,\"67\.0\ \%\"\)\,main\=\"Genome\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
+\>\ x\<\-c\(0\.000000\,1\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 1\.9\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 1\.7\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 1\.6\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 1\.8\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 1\.5\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 1\.4\ \%\"\,\"5\'UTR\:\ 0\.2\ \%\"\,\"3\'UTR\:\ 1\.4\ \%\"\,\"Coding\ exon\:\ 2\.3\ \%\"\,\"Intron\:\ 19\.3\ \%\"\,\"Distal\ intergenic\:\ 67\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ x\<\-c\(0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,1\.000000\)
+\>\ pie\(x\=x\,labels\=c\(\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"100\.0\ \%\"\)\,main\=\"ChIP\"\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,clockwise\=TRUE\,border\=FALSE\,radius\=0\.9\,cex\=0\.8\,init\.angle\=90\,density\=100\)
+\>\ x\<\-c\(0\.000000\,1\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"5\'UTR\:\ 0\.000\ \%\"\,\"3\'UTR\:\ 0\.000\ \%\"\,\"Coding\ exon\:\ 0\.000\ \%\"\,\"Intron\:\ 0\.000\ \%\"\,\"Distal\ intergenic\:\ 100\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
+\>\ 
+\>\ \#\ 
+\>\ \#\ ChIP\ regions\ over\ the\ genome
+\>\ \#\ 
+\>\ 
+\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ layout\(matrix\(c\(1\,\ 0\,\ 2\,\ 2\)\,\ 2\,\ 2\,\ byrow\ \=\ TRUE\)\,widths\=c\(1\,\ 1\)\,heights\=c\(1\,\ 5\)\)
+\>\ x\<\-c\(0\.000000\,0\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"Distribution\ of\ Peak\ Heights\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(0\.000000\,0\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\,cex\=0\.9\)
+\>\ x\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,1\.000000\,1\.000000\)
+\>\ polygon\(x\,y\,col\=c\(\"black\"\)\)
+\>\ x\ \<\-\ c\(0\.000000\)
+\>\ y\<\-c\(0\.800000\)
+\>\ lines\(x\,\ y\,xlim\=c\(0\,\ 0\.0\)\,ylim\=c\(0\,\ 1\)\,type\=\"l\"\,col\=c\(\"cyan\"\)\,lwd\=2\)
+\>\ x\<\-c\(0\.000000\,4127518\.000000\)
+\>\ y\<\-c\(0\.855556\,1\.144444\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"ChIP\ Regions\ \(Peaks\)\ over\ Chromosomes\"\,xlab\=\"Chromosome\ Size\ \(bp\)\"\,ylab\=\"Chromosome\"\,xlim\=c\(0\.000000\,4127518\.000000\)\,ylim\=c\(0\.855556\,1\.144444\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\)
+\>\ start\ \<\-\ c\(4119129\)
+\>\ end\ \<\-\ c\(4119130\)
+\>\ vals\ \<\-\ c\(0\.0\)
+\>\ vals\[vals\ \>\ 0\.0\]\ \<\-\ 0\.0
+\>\ vals\[vals\ \<\ 0\]\ \<\-\ 0
+\>\ heights\ \<\-\ 0\.288889\ \*\ \(\(vals\ \-\ 0\)\/\(0\.0\ \-\ 0\)\)\ \+\ 0\.855555555556
+\>\ for\ \(i\ in\ 1\:length\(heights\)\)\ \{
+\+\ \	polygon\(x\=c\(start\[i\]\,\ end\[i\]\,\ end\[i\]\,\ start\[i\]\)\,\ y\=c\(0\.855555555556\,\ 0\.855555555556\,\ heights\[i\]\,\ heights\[i\]\)\,\ col\=c\(\"\#CC0000\"\)\,\ border\=c\(\"\#CC0000\"\)\)
+\+\ \}
+\>\ mtext\(\"26\"\,side\=2\,line\=0\,outer\=FALSE\,at\=1\.0\)
+\>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ layout\(matrix\(c\(1\,\ 2\,\ 3\,\ 3\,\ 4\,\ 5\)\,\ 3\,\ 2\,\ byrow\ \=\ TRUE\)\,widths\=c\(1\,\ 1\)\,heights\=c\(1\,\ 1\,\ 1\)\)
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+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Profile\ near\ TSS\"\,xlab\=\"Relative\ Distance\ to\ TSS\ \(bp\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ abline\(v\=0\.000000\,lty\=2\,col\=c\(\"black\"\)\)
+\>\ x\<\-c\(\-3000\.000000\,\-2950\.000000\,\-2900\.000000\,\-2850\.000000\,\-2800\.000000\,\-2750\.000000\,\-2700\.000000\,\-2650\.000000\,\-2600\.000000\,\-2550\.000000\,\-2500\.000000\,\-2450\.000000\,\-2400\.000000\,\-2350\.000000\,\-2300\.000000\,\-2250\.000000\,\-2200\.000000\,\-2150\.000000\,\-2100\.000000\,\-2050\.000000\,\-2000\.000000\,\-1950\.000000\,\-1900\.000000\,\-1850\.000000\,\-1800\.000000\,\-1750\.000000\,\-1700\.000000\,\-1650\.000000\,\-1600\.000000\,\-1550\.000000\,\-1500\.000000\,\-1450\.000000\,\-1400\.000000\,\-1350\.000000\,\-1300\.000000\,\-1250\.000000\,\-1200\.000000\,\-1150\.000000\,\-1100\.000000\,\-1050\.000000\,\-1000\.000000\,\-950\.000000\,\-900\.000000\,\-850\.000000\,\-800\.000000\,\-750\.000000\,\-700\.000000\,\-650\.000000\,\-600\.000000\,\-550\.000000\,\-500\.000000\,\-450\.000000\,\-400\.000000\,\-350\.000000\,\-300\.000000\,\-250\.000000\,\-200\.000000\,\-150\.000000\,\-100\.000000\,\-50\.000000\,0\.000000\,50\.000000\,100\.000000\,150\.000000\,200\.000000\,250\.000000\,300\.000000\,350\.000000\,400\.000000\,450\.000000\,500\.000000\,550\.000000\,600\.000000\,650\.000000\,700\.000000\,750\.000000\,800\.000000\,850\.000000\,900\.000000\,950\.000000\,1000\.000000\,1050\.000000\,1100\.000000\,1150\.000000\,1200\.000000\,1250\.000000\,1300\.000000\,1350\.000000\,1400\.000000\,1450\.000000\,1500\.000000\,1550\.000000\,1600\.000000\,1650\.000000\,1700\.000000\,1750\.000000\,1800\.000000\,1850\.000000\,1900\.000000\,1950\.000000\,2000\.000000\,2050\.000000\,2100\.000000\,2150\.000000\,2200\.000000\,2250\.000000\,2300\.000000\,2350\.000000\,2400\.000000\,2450\.000000\,2500\.000000\,2550\.000000\,2600\.000000\,2650\.000000\,2700\.000000\,2750\.000000\,2800\.000000\,2850\.000000\,2900\.000000\,2950\.000000\,3000\.000000\)
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+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Profile\ near\ TTS\"\,xlab\=\"Relative\ Distance\ to\ TTS\ \(bp\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ abline\(v\=0\.000000\,lty\=2\,col\=c\(\"black\"\)\)
+\>\ x\<\-c\(\-1000\.000000\,\-950\.000000\,\-900\.000000\,\-850\.000000\,\-800\.000000\,\-750\.000000\,\-700\.000000\,\-650\.000000\,\-600\.000000\,\-550\.000000\,\-500\.000000\,\-450\.000000\,\-400\.000000\,\-350\.000000\,\-300\.000000\,\-250\.000000\,\-200\.000000\,\-150\.000000\,\-100\.000000\,\-50\.000000\,0\.000000\,50\.000000\,100\.000000\,150\.000000\,200\.000000\,250\.000000\,300\.000000\,350\.000000\,400\.000000\,450\.000000\,500\.000000\,550\.000000\,600\.000000\,650\.000000\,700\.000000\,750\.000000\,800\.000000\,850\.000000\,900\.000000\,950\.000000\,1000\.000000\,1050\.000000\,1100\.000000\,1150\.000000\,1200\.000000\,1250\.000000\,1300\.000000\,1350\.000000\,1400\.000000\,1450\.000000\,1500\.000000\,1550\.000000\,1600\.000000\,1650\.000000\,1700\.000000\,1750\.000000\,1800\.000000\,1850\.000000\,1900\.000000\,1950\.000000\,2000\.000000\,2050\.000000\,2100\.000000\,2150\.000000\,2200\.000000\,2250\.000000\,2300\.000000\,2350\.000000\,2400\.000000\,2450\.000000\,2500\.000000\,2550\.000000\,2600\.000000\,2650\.000000\,2700\.000000\,2750\.000000\,2800\.000000\,2850\.000000\,2900\.000000\,2950\.000000\,3000\.000000\,3050\.000000\,3100\.000000\,3150\.000000\,3200\.000000\,3250\.000000\,3300\.000000\,3350\.000000\,3400\.000000\,3450\.000000\,3500\.000000\,3550\.000000\,3600\.000000\,3650\.000000\,3700\.000000\,3750\.000000\,3800\.000000\,3850\.000000\,3900\.000000\,3950\.000000\,4000\.000000\)
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+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Gene\ Profile\"\,xlab\=\"Upstream\ \(bp\)\,\ 3000\ bp\ of\ Meta\-gene\,\ Downstream\ \(bp\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ abline\(v\=0\.000000\,lty\=2\,col\=c\(\"black\"\)\)
+\>\ abline\(v\=3000\.000000\,lty\=2\,col\=c\(\"black\"\)\)
+\>\ x\<\-c\(0\.000000\,3\.333333\,6\.666667\,10\.000000\,13\.333333\,16\.666667\,20\.000000\,23\.333333\,26\.666667\,30\.000000\,33\.333333\,36\.666667\,40\.000000\,43\.333333\,46\.666667\,50\.000000\,53\.333333\,56\.666667\,60\.000000\,63\.333333\,66\.666667\,70\.000000\,73\.333333\,76\.666667\,80\.000000\,83\.333333\,86\.666667\,90\.000000\,93\.333333\,96\.666667\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Concatenated\ Exon\ Profile\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,20000\.000000\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ x\<\-c\(0\.000000\,3\.333333\,6\.666667\,10\.000000\,13\.333333\,16\.666667\,20\.000000\,23\.333333\,26\.666667\,30\.000000\,33\.333333\,36\.666667\,40\.000000\,43\.333333\,46\.666667\,50\.000000\,53\.333333\,56\.666667\,60\.000000\,63\.333333\,66\.666667\,70\.000000\,73\.333333\,76\.666667\,80\.000000\,83\.333333\,86\.666667\,90\.000000\,93\.333333\,96\.666667\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Concatenated\ Intron\ Profile\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,20000\.000000\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ par\(mfrow\=c\(3\,\ 2\)\,mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
+\>\ x\<\-c\(\-3\.000000\,3\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ x\<\-c\(\-3\.000000\,3\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ x\<\-c\(\-3\.000000\,3\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ x\<\-c\(\-3\.000000\,3\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ x\<\-c\(\-3\.000000\,3\.000000\)
+\>\ y\<\-c\(0\.000000\,1\.000000\)
+\>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
+\>\ x\<\-c\(0\.000000\,4\.761905\,9\.523810\,14\.285714\,19\.047619\,23\.809524\,28\.571429\,33\.333333\,38\.095238\,42\.857143\,47\.619048\,52\.380952\,57\.142857\,61\.904762\,66\.666667\,71\.428571\,76\.190476\,80\.952381\,85\.714286\,90\.476190\,95\.238095\,100\.000000\)
+\>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\)
+\>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Intron\ Profile
+\+\ \(685\ \<\=\ length\ \<\ 2653\ bp\)\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,24000\.000000\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
+\>\ dev\.off\(\)
+null\ device\ 
+\ \ \ \ \ \ \ \ \ \ 1\ 
+\>\ 
+INFO\ \ \@\ .*\ \#\.\.\.\ cong\!\ See\ ceas\.pdf\ for\ the\ graphical\ results\ of\ CEAS\!\ 
Binary file test-data/ceas_out3.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out3.xls	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,133 @@
+# RefSeq: RefSeq ID
+# chr: chromosome of a RefSeq gene
+# txStart: 5' end of a RefSeq gene
+# txEnd: 3' end site of a RefSeq gene
+# strand: strand of a RefSeq gene
+# dist u TSS: Distance to the nearest ChIP region's center upstream of transcription start site (bp)
+# dist d TSS: Distance to the nearest ChIP region's center downstream of transcription start site (bp)
+# dist u TTS: Distance to the nearest ChIP region's center upstream of transcription end site (bp)
+# dist d TTS: Distance to the nearest ChIP region's center downstream of transcription end (bp)
+# 3000bp u TSS: Occupancy rate of ChIP region in 3000bp upstream of transcription start site (0.0 - 1.0)
+# 3000bp d TSS: Occupancy rate of ChIP region in 3000bp downstream of transcription start site (0.0 - 1.0)
+# 1/3 gene: Occupancy rate of ChIP region in 1/3 gene (0.0 - 1.0)
+# 2/3 gene: Occupancy rate of ChIP region in 2/3 gene (0.0 - 1.0)
+# 3/3 gene: Occupancy rate of ChIP region in 3/3 gene (0.0 - 1.0)
+# 3000bp d TTS: Occupancy rate of ChIP region in 3000bp downstream of transcriptino end (0.0 - 1.0)
+# exons: Occupancy rate of ChIP regions in exons (0.0-1.0)
+# Note that txStart and txEnd indicate 5' and 3' ends of genes whereas TSS and TTS transcription start and end sites in consideration of strand.
+#name	chr	txStart	txEnd	strand	dist u TSS	dist d TSS	dist u TTS	dist d TTS	3000bp u TSS	3000bp d TSS	1/3 gene	2/3 gene	3/3 gene	3000bp d TTS	exons
+NM_001031576	chr26	19281	27136	+	NA	4099848	NA	4091993	0	0	0	0	0	0	0
+NM_204615	chr26	57466	61594	-	4057535	NA	4061663	NA	0	0	0	0	0	0	0
+NM_001005431	chr26	65800	76175	-	4042954	NA	4053329	NA	0	0	0	0	0	0	0
+NM_001145491	chr26	91618	92166	-	4026963	NA	4027511	NA	0	0	0	0	0	0	0
+NM_204398	chr26	93069	97423	+	NA	4026060	NA	4021706	0	0	0	0	0	0	0
+NM_001305147	chr26	254661	282571	+	NA	3864468	NA	3836558	0	0	0	0	0	0	0
+NM_001305148	chr26	254661	282571	+	NA	3864468	NA	3836558	0	0	0	0	0	0	0
+NM_001012868	chr26	350397	355252	-	3763877	NA	3768732	NA	0	0	0	0	0	0	0
+NM_001031030	chr26	479573	493561	+	NA	3639556	NA	3625568	0	0	0	0	0	0	0
+NM_001305140	chr26	520705	526012	+	NA	3598424	NA	3593117	0	0	0	0	0	0	0
+NM_001031029	chr26	537101	565572	+	NA	3582028	NA	3553557	0	0	0	0	0	0	0
+NM_205248	chr26	537250	760479	+	NA	3581879	NA	3358650	0	0	0	0	0	0	0
+NM_204727	chr26	662969	683066	-	3436063	NA	3456160	NA	0	0	0	0	0	0	0
+NR_105475	chr26	669012	669122	-	3450007	NA	3450117	NA	0	0	0	0	0	0	0
+NM_205449	chr26	785617	794076	+	NA	3333512	NA	3325053	0	0	0	0	0	0	0
+NM_204681	chr26	897458	902049	-	3217080	NA	3221671	NA	0	0	0	0	0	0	0
+NM_001278156	chr26	905313	917094	-	3202035	NA	3213816	NA	0	0	0	0	0	0	0
+NM_204184	chr26	960209	964268	-	3154861	NA	3158920	NA	0	0	0	0	0	0	0
+NM_204316	chr26	974223	991244	+	NA	3144906	NA	3127885	0	0	0	0	0	0	0
+NM_001031028	chr26	993815	1003847	-	3115282	NA	3125314	NA	0	0	0	0	0	0	0
+NM_001006392	chr26	1024606	1047756	-	3071373	NA	3094523	NA	0	0	0	0	0	0	0
+NM_001039596	chr26	1073550	1080033	-	3039096	NA	3045579	NA	0	0	0	0	0	0	0
+NM_001031027	chr26	1090460	1096137	+	NA	3028669	NA	3022992	0	0	0	0	0	0	0
+NM_001031026	chr26	1096566	1104751	-	3014378	NA	3022563	NA	0	0	0	0	0	0	0
+NM_001030913	chr26	1122296	1132596	+	NA	2996833	NA	2986533	0	0	0	0	0	0	0
+NM_001171886	chr26	1220031	1222791	-	2896338	NA	2899098	NA	0	0	0	0	0	0	0
+NM_205054	chr26	1229703	1232833	+	NA	2889426	NA	2886296	0	0	0	0	0	0	0
+NM_204462	chr26	1234686	1236536	-	2882593	NA	2884443	NA	0	0	0	0	0	0	0
+NM_204463	chr26	1265724	1267989	-	2851140	NA	2853405	NA	0	0	0	0	0	0	0
+NM_001030378	chr26	1289091	1290386	-	2828743	NA	2830038	NA	0	0	0	0	0	0	0
+NM_001195554	chr26	1382510	1388447	+	NA	2736619	NA	2730682	0	0	0	0	0	0	0
+NM_001012548	chr26	1406905	1428443	+	NA	2712224	NA	2690686	0	0	0	0	0	0	0
+NR_031486	chr26	1442696	1442779	-	2676350	NA	2676433	NA	0	0	0	0	0	0	0
+NR_031487	chr26	1442896	1442979	-	2676150	NA	2676233	NA	0	0	0	0	0	0	0
+NM_205250	chr26	1472137	1474003	+	NA	2646992	NA	2645126	0	0	0	0	0	0	0
+NR_105486	chr26	1566398	1566508	-	2552621	NA	2552731	NA	0	0	0	0	0	0	0
+NM_001160320	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001004709	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160324	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001004493	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160323	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160322	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001160321	chr26	1697226	1773801	+	NA	2421903	NA	2345328	0	0	0	0	0	0	0
+NM_001004395	chr26	1776431	1800083	+	NA	2342698	NA	2319046	0	0	0	0	0	0	0
+NM_001030914	chr26	1811042	1820368	-	2298761	NA	2308087	NA	0	0	0	0	0	0	0
+NM_204506	chr26	1823407	1843085	-	2276044	NA	2295722	NA	0	0	0	0	0	0	0
+NR_031488	chr26	1925941	1926037	-	2193092	NA	2193188	NA	0	0	0	0	0	0	0
+NM_213581	chr26	2070404	2084478	-	2034651	NA	2048725	NA	0	0	0	0	0	0	0
+NR_035298	chr26	2086590	2086691	-	2032438	NA	2032539	NA	0	0	0	0	0	0	0
+NR_105470	chr26	2094750	2094860	-	2024269	NA	2024379	NA	0	0	0	0	0	0	0
+NM_001030915	chr26	2117140	2128322	-	1990807	NA	2001989	NA	0	0	0	0	0	0	0
+NM_001031498	chr26	2175178	2177159	-	1941970	NA	1943951	NA	0	0	0	0	0	0	0
+NM_001008452	chr26	2305308	2315138	+	NA	1813821	NA	1803991	0	0	0	0	0	0	0
+NM_001006322	chr26	2315293	2325130	-	1793999	NA	1803836	NA	0	0	0	0	0	0	0
+NM_001004414	chr26	2373245	2375480	-	1743649	NA	1745884	NA	0	0	0	0	0	0	0
+NM_001044644	chr26	2390696	2401255	-	1717874	NA	1728433	NA	0	0	0	0	0	0	0
+NM_001031499	chr26	2425841	2429413	-	1689716	NA	1693288	NA	0	0	0	0	0	0	0
+NM_001033642	chr26	2445710	2453125	+	NA	1673419	NA	1666004	0	0	0	0	0	0	0
+NM_001033643	chr26	2469318	2475028	+	NA	1649811	NA	1644101	0	0	0	0	0	0	0
+NM_204664	chr26	2498398	2509349	+	NA	1620731	NA	1609780	0	0	0	0	0	0	0
+NR_031489	chr26	2511657	2511746	-	1607383	NA	1607472	NA	0	0	0	0	0	0	0
+NR_031490	chr26	2512568	2512648	-	1606481	NA	1606561	NA	0	0	0	0	0	0	0
+NR_105523	chr26	2669792	2669902	-	1449227	NA	1449337	NA	0	0	0	0	0	0	0
+NR_031491	chr26	2896046	2896142	+	NA	1223083	NA	1222987	0	0	0	0	0	0	0
+NM_001190924	chr26	2961382	2962268	+	NA	1157747	NA	1156861	0	0	0	0	0	0	0
+NM_001007881	chr26	2999189	3002725	+	NA	1119940	NA	1116404	0	0	0	0	0	0	0
+NM_204320	chr26	3006741	3011817	-	1107312	NA	1112388	NA	0	0	0	0	0	0	0
+NM_001030916	chr26	3035271	3039335	-	1079794	NA	1083858	NA	0	0	0	0	0	0	0
+NM_204151	chr26	3047964	3050306	-	1068823	NA	1071165	NA	0	0	0	0	0	0	0
+NM_204326	chr26	3124816	3214381	-	904748	NA	994313	NA	0	0	0	0	0	0	0
+NM_204336	chr26	3320769	3332327	+	NA	798360	NA	786802	0	0	0	0	0	0	0
+NM_204622	chr26	3339753	3358863	-	760266	NA	779376	NA	0	0	0	0	0	0	0
+NM_205515	chr26	3359016	3368964	+	NA	760113	NA	750165	0	0	0	0	0	0	0
+NM_001012843	chr26	3370712	3377196	+	NA	748417	NA	741933	0	0	0	0	0	0	0
+NM_001029849	chr26	3377655	3382628	-	736501	NA	741474	NA	0	0	0	0	0	0	0
+NM_001006323	chr26	3439841	3454783	-	664346	NA	679288	NA	0	0	0	0	0	0	0
+NR_035162	chr26	3455233	3455324	+	NA	663896	NA	663805	0	0	0	0	0	0	0
+NM_001012697	chr26	3516478	3545774	+	NA	602651	NA	573355	0	0	0	0	0	0	0
+NM_001030917	chr26	3590932	3597509	-	521620	NA	528197	NA	0	0	0	0	0	0	0
+NM_001031500	chr26	3597231	3600802	+	NA	521898	NA	518327	0	0	0	0	0	0	0
+NM_001040018	chr26	3629575	3631171	+	NA	489554	NA	487958	0	0	0	0	0	0	0
+NM_001257295	chr26	3698350	3701362	-	417767	NA	420779	NA	0	0	0	0	0	0	0
+NM_001257296	chr26	3701377	3715857	-	403272	NA	417752	NA	0	0	0	0	0	0	0
+NM_001012549	chr26	3735643	3742472	-	376657	NA	383486	NA	0	0	0	0	0	0	0
+NM_001030918	chr26	3742618	3760175	-	358954	NA	376511	NA	0	0	0	0	0	0	0
+NM_001006324	chr26	3760758	3765368	-	353761	NA	358371	NA	0	0	0	0	0	0	0
+NM_205063	chr26	3809805	3812700	+	NA	309324	NA	306429	0	0	0	0	0	0	0
+NM_001293109	chr26	3859074	3879130	-	239999	NA	260055	NA	0	0	0	0	0	0	0
+NM_001293108	chr26	3859074	3882051	-	237078	NA	260055	NA	0	0	0	0	0	0	0
+NR_102328	chr26	3916006	3918143	-	200986	NA	203123	NA	0	0	0	0	0	0	0
+NM_204728	chr26	3920817	3937442	-	181687	NA	198312	NA	0	0	0	0	0	0	0
+NM_001244905	chr26	4104910	4108376	+	NA	14219	NA	10753	0	0	0	0	0	0	0
+NM_001293166	chr26	4138324	4142325	-	NA	23196	NA	19195	0	0	0	0	0	0	0
+NM_001030919	chr26	4144091	4175943	+	24962	NA	56814	NA	0	0	0	0	0	0	0
+NM_001257297	chr26	4209891	4216177	+	90762	NA	97048	NA	0	0	0	0	0	0	0
+NM_001257298	chr26	4218028	4238067	+	98899	NA	118938	NA	0	0	0	0	0	0	0
+NM_205490	chr26	4375371	4380959	-	NA	261830	NA	256242	0	0	0	0	0	0	0
+NM_001305129	chr26	4391940	4397490	+	272811	NA	278361	NA	0	0	0	0	0	0	0
+NM_001271612	chr26	4433568	4438784	+	314439	NA	319655	NA	0	0	0	0	0	0	0
+NM_001030920	chr26	4498991	4730550	+	379862	NA	611421	NA	0	0	0	0	0	0	0
+NM_001030921	chr26	4541748	4544997	-	NA	425868	NA	422619	0	0	0	0	0	0	0
+NM_001006325	chr26	4548211	4559974	+	429082	NA	440845	NA	0	0	0	0	0	0	0
+NM_001037832	chr26	4571684	4576072	-	NA	456943	NA	452555	0	0	0	0	0	0	0
+NM_001080870	chr26	4578266	4580646	-	NA	461517	NA	459137	0	0	0	0	0	0	0
+NM_001080868	chr26	4578266	4580647	-	NA	461518	NA	459137	0	0	0	0	0	0	0
+NM_001030922	chr26	4730394	4744364	-	NA	625235	NA	611265	0	0	0	0	0	0	0
+NM_204877	chr26	4751619	4755464	-	NA	636335	NA	632490	0	0	0	0	0	0	0
+NM_001302134	chr26	4791084	4792014	+	671955	NA	672885	NA	0	0	0	0	0	0	0
+NM_001006327	chr26	4828534	4833077	-	NA	713948	NA	709405	0	0	0	0	0	0	0
+NM_001008453	chr26	4838545	4850970	-	NA	731841	NA	719416	0	0	0	0	0	0	0
+NM_001030923	chr26	4876559	4884910	+	757430	NA	765781	NA	0	0	0	0	0	0	0
+NM_204429	chr26	4897094	4901738	-	NA	782609	NA	777965	0	0	0	0	0	0	0
+NM_204967	chr26	4946735	4952662	-	NA	833533	NA	827606	0	0	0	0	0	0	0
+NM_204473	chr26	4990765	4993729	+	871636	NA	874600	NA	0	0	0	0	0	0	0
+NR_105623	chr26	5087926	5087980	-	NA	968851	NA	968797	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/galGal3.len	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,57 @@
+chr1	200994015
+chr2	154873767
+chr3	113657789
+chr4	94230402
+chrZ	74602320
+chrUn_random	63870806
+chr5	62238931
+chr7	38384769
+chr6	37400442
+chr8	30671729
+chr9	25554352
+chr10	22556432
+chr11	21928095
+chr12	20536687
+chr13	18911934
+chr14	15819469
+chr20	13986235
+chr15	12968165
+chr17	11182526
+chr18	10925261
+chr19	9939723
+chr21	6959642
+chr24	6400109
+chr23	6042217
+chr26	5102438
+chr27	4841970
+chr28	4512026
+chr22	3936574
+chr25	2031799
+chrE22C19W28_E50C23	895237
+chrW_random	729481
+chrE64_random	557643
+chr16	432983
+chr8_random	420759
+chrZ_random	346234
+chrW	259642
+chr16_random	246252
+chr1_random	222095
+chrE22C19W28_E50C23_random	191099
+chr4_random	180706
+chr22_random	156216
+chr2_random	142837
+chr28_random	105415
+chr7_random	104000
+chr25_random	80372
+chr20_random	75095
+chr11_random	72667
+chrE64	49846
+chr13_random	35775
+chr6_random	34212
+chr5_random	27907
+chrM	16775
+chr10_random	13679
+chr18_random	11891
+chr12_random	7060
+chr17_random	2911
+chr32	1028
Binary file test-data/galGal3.refGene has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ceas.loc.sample	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,17 @@
+#This is a sample file distributed with Galaxy that is used by the
+#ceas tool. The ceas.loc file has this format (white space 
+#characters are TAB characters):
+#
+#<unique_build>	<dbkey> <Description>	<PathToGdbFile>
+#
+#For example:
+#
+#hg18_illumina_pe	hg18	Human (hg18)	/home/galaxy/genomes/ceaslib/GeneTable/hg18
+#mm9_generic	mm9	Mouse (mm9)	/home/galaxy/genomes/ceaslib/GeneTable/mm9
+#...etc...
+#
+# The GDB files are sqlite databases containing the RefSeq genes for
+# the organism in question
+#
+#This file should be placed in galaxy's tool-data directory when the
+#ceas tool is installed.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="ceas_annotations" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/ceas.loc" />
+    </table>
+</tables>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="ceas_annotations" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+	<file path="${__HERE__}/test-data/ceas.loc" />
+    </table>
+</tables>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,114 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <!-- Local version of R 3.1.2 dependency -->
+  <package name="R" version="3.1.2">
+    <install version="1.0">
+      <actions>
+	<action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz</action>
+        <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
+        <action type="make_install" />
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+  </package>
+  <!-- Python mysqldb package -->
+  <package name="python_mysqldb" version="1.2.5">
+    <install version="1.0">
+      <actions>
+	<action type="download_by_url">https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip</action>
+        <action type="make_directory">$INSTALL_DIR/lib/python</action>
+        <action type="shell_command">
+          export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+          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">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>Installs Python module MySQLdb 1.2.5</readme>
+  </package>
+  <!-- bx_python
+       This is cribbed from devteam's 'package_bx_python_0_7' in the main
+       toolshed:
+       https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
+  -->
+  <package name="bx_python" version="0.7.1">
+    <install version="1.0">
+      <actions>
+        <action type="setup_virtualenv">
+numpy==1.7.1
+bx-python==0.7.1
+        </action>
+        <action type="set_environment">
+          <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>
+      Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be
+      accessed via BX_PYTHON_PATH.
+    </readme>
+  </package>
+  <!-- cistrome_ceas
+       Installs the version of CEAS package found in the Cistrome
+       distribution:
+       https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
+  -->
+  <package name="cistrome_ceas" version="1.0.2.d8c0751">
+    <install version="1.0">
+      <actions>
+	<action type="shell_command">
+	  hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas
+	</action>
+	<action type="shell_command">
+	  hg update d8c0751
+	</action>
+        <action type="make_directory">$INSTALL_DIR/lib/python</action>
+        <action type="shell_command">
+	  cd published-packages/CEAS/
+          export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+          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">$INSTALL_DIR/bin</environment_variable>
+        </action>
+      </actions>
+    </install>
+    <readme>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751,
+    datestamp 20140929), which includes ceasBW (a version of ceas which can
+    handle bigWig file input from MACS2.
+
+    Cistrome code is at
+    https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
+      
+    The CEAS code is under the published-packages/CEAS/ subdirectory
+
+    Cistrome data files and documentation can be found at
+    http://liulab.dfci.harvard.edu/CEAS/index.html
+    </readme>
+  </package>
+  <!-- fetchChromSize from UCSC tools -->
+  <package name="ucsc_fetchChromSizes" version="1.0">
+      <install version="1.0">
+        <actions>
+          <action type="download_binary">
+            <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes</url_template>
+          </action>
+          <action type="chmod">
+            <file mode="755">$INSTALL_DIR/fetchChromSizes</file>
+          </action>
+          <action type="set_environment">
+            <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+        </action>
+	</actions>
+      </install>
+    <readme>Installs the binary executable for the fetchChromSizes utility
+    from UCSC tools
+    </readme>
+  </package>
+</tool_dependency>