| Next changeset 1:df9033b88b53 (2016-08-11) |
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Uploaded initial version 1.0.2-2 |
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added:
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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| diff -r 000000000000 -r f411ce97a351 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Jun 30 07:08:05 2015 -0400 |
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| @@ -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. |
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| diff -r 000000000000 -r f411ce97a351 ceas_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ceas_wrapper.sh Tue Jun 30 07:08:05 2015 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r f411ce97a351 ceas_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ceas_wrapper.xml Tue Jun 30 07:08:05 2015 -0400 |
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| @@ -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>&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> |
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| diff -r 000000000000 -r f411ce97a351 data_manager/data_manager_ceas_fetch_annotations.py --- /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 |
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| @@ -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)) + |
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| diff -r 000000000000 -r f411ce97a351 data_manager/data_manager_ceas_fetch_annotations.xml --- /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 |
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| @@ -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> |
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| diff -r 000000000000 -r f411ce97a351 data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Tue Jun 30 07:08:05 2015 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r f411ce97a351 test-data/ceas.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ceas.loc Tue Jun 30 07:08:05 2015 -0400 |
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| @@ -0,0 +1,1 @@ +galGal3_test galGal3 galGal3 ${__HERE__}/galGal3.refGene |
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| diff -r 000000000000 -r f411ce97a351 test-data/ceas_in.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ceas_in.bed Tue Jun 30 07:08:05 2015 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chr26 4119129 4119130 test_MACS2.1.0_peak_1 2.51561 |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_in.bigwig |
| b |
| Binary file test-data/ceas_in.bigwig has changed |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_in.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ceas_in.wig Tue Jun 30 07:08:05 2015 -0400 |
| b |
| b'@@ -0,0 +1,4312 @@\n+track type=wiggle_0 name="test_MACS2.1.0_treat_pileup.bdg" description="test_MACS2.1.0_treat_pileup.bdg" visibility=full\n+fixedStep chrom=chr26 start=0 step=1000 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| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ceas_out1.log Tue Jun 30 07:08:05 2015 -0400 |
| [ |
| b'@@ -0,0 +1,184 @@\n+ceas -- 0.9.9.7 (package version 1.0.2)\n+INFO @ Tue, 23 Jun 2015 09:12:22: \n+# ARGUMENTS: \n+# name = ceas\n+# gene annotation table = galGal3.refGene\n+# BED file = ceas_in.bed\n+# WIG file = None\n+# extra BED file = None\n+# ChIP annotation = On\n+# gene-centered annotation = On\n+# average profiling = Off\n+# dump profiles = Off\n+# re-annotation for genome background (ChIP region annotation) = False\n+# promoter sizes (ChIP region annotation) = 1000,2000,3000 bp\n+# downstream sizes (ChIP region annotation) = 1000,2000,3000 bp\n+# bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp\n+# span size (gene-centered annotation) = 3000 bp \n+INFO @ Tue, 23 Jun 2015 09:12:22: #1 read the gene table... \n+INFO @ Tue, 23 Jun 2015 09:12:22: #2 read the bed file of ChIP regions... \n+INFO @ Tue, 23 Jun 2015 09:12:22: #3 perform gene-centered annotation... \n+INFO @ Tue, 23 Jun 2015 09:12:22: #4 See ceas.xls for gene-centered annotation! \n+INFO @ Tue, 23 Jun 2015 09:12:22: #5 read the pre-computed genome bg annotation... \n+INFO @ Tue, 23 Jun 2015 09:12:22: #6 perform ChIP region annotation... \n+INFO @ Tue, 23 Jun 2015 09:12:22: #7 write a R script of ChIP region annotation... \n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-redhat-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> # ARGUMENTS: \n+> # name = ceas\n+> # gene annotation table = galGal3.refGene\n+> # BED file = ceas_in.bed\n+> # WIG file = None\n+> # extra BED file = None\n+> # ChIP annotation = On\n+> # gene-centered annotation = On\n+> # average profiling = Off\n+> # dump profiles = Off\n+> # re-annotation for genome background (ChIP region annotation) = False\n+> # promoter sizes (ChIP region annotation) = 1000,2000,3000 bp\n+> # downstream sizes (ChIP region annotation) = 1000,2000,3000 bp\n+> # bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp\n+> # span size (gene-centered annotation) = 3000 bp\n+> pdf("ceas.pdf",height=11.5,width=8.5)\n+> \n+> # 09:12:22 Tue, 23 Jun 2015\n+> # \n+> # ChIP annotation\n+> # \n+> \n+> \n+> # \n+> # Chromosomal Distribution\n+> # \n+> \n+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))\n+> r0<-c(100.0)\n+> r1<-c(100.0)\n+> height<-rbind(r0,r1)\n+> names=c("26")\n+> 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)\n+> text(x=c(100.0),y=mp[1,],label=c("100.0 %"),pos=4,offset=0.2,cex=0.9)\n+> text(x=c(100.0),y=mp[2,],label=c("100.0 % (<=4.9e-324)"),pos=4,offset=0.2,cex=0.9)\n+> legend("right",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")\n+> \n+> # \n+> # Promoter,Bipromoter,Downstream, Gene and Regions of interest\n+> # \n+> \n+> par(mfrow=c(4, 1),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))\n+> r0<-c(1.8532425688606797, 3.616851183410451, 5.322318854623416)\n+> r1<-c(0.0, 0.0, 0.0)\n+> height<-rbind(r0,r1)\n+> names=c("<=1000 bp","<=2000 bp","<=3000 bp")\n+> 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)\n+> 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)\n+> text(x=mp[2,],y=c(0.0, 0.0, 0.0),label=c("0.000 %\n++ (0.981)","0.000 %\n++ (0.96'..b'hics in case a value is too small\n+> # Thus, look at the labels of the pie chart to get the real percentage values\n+> # \n+> \n+> par(mfcol=c(2, 2),mar=c(3, 3, 4, 2.8),oma=c(4, 2, 4, 2))\n+> x<-c(0.018532,0.017055,0.016037,0.017830,0.015092,0.014051,0.010000,0.013833,0.023014,0.192592,0.670292)\n+> 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)\n+> x<-c(0.000000,1.000000)\n+> y<-c(0.000000,1.000000)\n+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")\n+> 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")\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)\n+> 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)\n+> x<-c(0.000000,1.000000)\n+> y<-c(0.000000,1.000000)\n+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")\n+> 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")\n+> \n+> # \n+> # ChIP regions over the genome\n+> # \n+> \n+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))\n+> layout(matrix(c(1, 0, 2, 2), 2, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 5))\n+> x<-c(0.000000,2.515610)\n+> y<-c(0.000000,1.000000)\n+> 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)\n+> x<-c(0.000000,2.515610,2.515610,0.000000)\n+> y<-c(0.000000,0.000000,1.000000,1.000000)\n+> polygon(x,y,col=c("black"))\n+> 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)\n+> 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)\n+> lines(x, y,xlim=c(0, 2.51561),ylim=c(0, 1),type="l",col=c("cyan"),lwd=2)\n+> x<-c(4119129.000000,4119130.000000)\n+> y<-c(0.855556,1.144444)\n+> 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")\n+> start <- c(4119129)\n+> end <- c(4119130)\n+> vals <- c(2.51561)\n+> vals[vals > 2.51561] <- 2.51561\n+> vals[vals < 0] <- 0\n+> heights <- 0.288889 * ((vals - 0)/(2.51561 - 0)) + 0.855555555556\n+> for (i in 1:length(heights)) {\n++ \tpolygon(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"))\n++ }\n+> mtext("26",side=2,line=0,outer=FALSE,at=1.0)\n+> dev.off()\n+null device \n+ 1 \n+> \n+INFO @ Tue, 23 Jun 2015 09:12:22: #... cong! See ceas.pdf for the graphical results of CEAS! \n' |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out1.log.re_match --- /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 |
| [ |
| b'@@ -0,0 +1,184 @@\n+ceas\\ \\-\\-\\ 0\\.9\\.9\\.7\\ \\(package\\ version\\ 1\\.0\\.2\\)\n+INFO\\ \\ \\@\\ .*\n+\\#\\ ARGUMENTS\\:\\ \n+\\#\\ name\\ \\=\\ ceas\n+\\#\\ gene\\ annotation\\ table\\ \\=\\ .*galGal3\\.refGene\n+\\#\\ BED\\ file\\ \\=\\ .*\n+\\#\\ WIG\\ file\\ \\=\\ None\n+\\#\\ extra\\ BED\\ file\\ \\=\\ None\n+\\#\\ ChIP\\ annotation\\ \\=\\ On\n+\\#\\ gene\\-centered\\ annotation\\ \\=\\ \\ On\n+\\#\\ average\\ profiling\\ \\=\\ Off\n+\\#\\ dump\\ profiles\\ \\=\\ Off\n+\\#\\ re\\-annotation\\ for\\ genome\\ background\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ False\n+\\#\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\#\\ downstream\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\#\\ bidrectional\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 2500\\,5000\\ bp\n+\\#\\ span\\ size\\ \\(gene\\-centered\\ annotation\\)\\ \\=\\ 3000\\ bp\\ \n+INFO\\ \\ \\@\\ .*\\ \\#1\\ read\\ the\\ gene\\ table\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#2\\ read\\ the\\ bed\\ file\\ of\\ ChIP\\ regions\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#3\\ perform\\ gene\\-centered\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#4\\ See\\ ceas\\.xls\\ for\\ gene\\-centered\\ annotation\\!\\ \n+INFO\\ \\ \\@\\ .*\\ \\#5\\ read\\ the\\ pre\\-computed\\ genome\\ bg\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#6\\ perform\\ ChIP\\ region\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#7\\ write\\ a\\ R\\ script\\ of\\ ChIP\\ region\\ annotation\\.\\.\\.\\ \n+\n+R\\ version\\ 3\\.1\\.2\\ \\(2014\\-10\\-31\\)\\ \\-\\-\\ \\"Pumpkin\\ Helmet\\"\n+Copyright\\ \\(C\\)\\ 2014\\ The\\ R\\ Foundation\\ for\\ Statistical\\ Computing\n+Platform\\:\\ .*\n+\n+R\\ is\\ free\\ software\\ and\\ comes\\ with\\ ABSOLUTELY\\ NO\\ WARRANTY\\.\n+You\\ are\\ welcome\\ to\\ redistribute\\ it\\ under\\ certain\\ conditions\\.\n+Type\\ \\\'license\\(\\)\\\'\\ or\\ \\\'licence\\(\\)\\\'\\ for\\ distribution\\ details\\.\n+\n+\\ \\ Natural\\ language\\ support\\ but\\ running\\ in\\ an\\ English\\ locale\n+\n+R\\ is\\ a\\ collaborative\\ project\\ with\\ many\\ contributors\\.\n+Type\\ \\\'contributors\\(\\)\\\'\\ for\\ more\\ information\\ and\n+\\\'citation\\(\\)\\\'\\ on\\ how\\ to\\ cite\\ R\\ or\\ R\\ packages\\ in\\ publications\\.\n+\n+Type\\ \\\'demo\\(\\)\\\'\\ for\\ some\\ demos\\,\\ \\\'help\\(\\)\\\'\\ for\\ on\\-line\\ help\\,\\ or\n+\\\'help\\.start\\(\\)\\\'\\ for\\ an\\ HTML\\ browser\\ interface\\ to\\ help\\.\n+Type\\ \\\'q\\(\\)\\\'\\ to\\ quit\\ R\\.\n+\n+\\>\\ \\#\\ ARGUMENTS\\:\\ \n+\\>\\ \\#\\ name\\ \\=\\ ceas\n+\\>\\ \\#\\ gene\\ annotation\\ table\\ \\=\\ .*galGal3\\.refGene\n+\\>\\ \\#\\ BED\\ file\\ \\=\\ .*\n+\\>\\ \\#\\ WIG\\ file\\ \\=\\ None\n+\\>\\ \\#\\ extra\\ BED\\ file\\ \\=\\ None\n+\\>\\ \\#\\ ChIP\\ annotation\\ \\=\\ On\n+\\>\\ \\#\\ gene\\-centered\\ annotation\\ \\=\\ \\ On\n+\\>\\ \\#\\ average\\ profiling\\ \\=\\ Off\n+\\>\\ \\#\\ dump\\ profiles\\ \\=\\ Off\n+\\>\\ \\#\\ re\\-annotation\\ for\\ genome\\ background\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ False\n+\\>\\ \\#\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\>\\ \\#\\ downstream\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\>\\ \\#\\ bidrectional\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 2500\\,5000\\ bp\n+\\>\\ \\#\\ span\\ size\\ \\(gene\\-centered\\ annotation\\)\\ \\=\\ 3000\\ bp\n+\\>\\ pdf\\(\\"ceas\\.pdf\\"\\,height\\=11\\.5\\,width\\=8\\.5\\)\n+\\>\\ \n+\\>\\ \\#\\ .*\n+\\>\\ \\#\\ \n+\\>\\ \\#\\ ChIP\\ annotation\n+\\>\\ \\#\\ \n+\\>\\ \n+\\>\\ \n+\\>\\ \\#\\ \n+\\>\\ \\#\\ Chromosomal\\ Distribution\n+\\>\\ \\#\\ \n+\\>\\ \n+\\>\\ par\\(mar\\=c\\(4\\,\\ 4\\,\\ 5\\,\\ 3\\.8\\)\\,oma\\=c\\(4\\,\\ 2\\,\\ 4\\,\\ 2\\)\\)\n+\\>\\ r0\\<\\-c\\(100\\.0\\)\n+\\>\\ r1\\<\\-c\\(100\\.0\\)\n+\\>\\ height\\<\\-rbind\\(r0\\,r1\\)\n+\\>\\ names\\=c\\(\\"26\\"\\)\n+\\>\\ 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\\)\n+\\>\\ text\\(x\\=c\\(100\\.0\\)\\,y\\=mp\\[1\\,\\]\\,label\\=c\\(\\"100\\.0\\ \\%\\"\\)\\,pos\\=4\\,offset\\=0\\.2\\,cex\\=0\\.9\\)\n+\\>\\ text\\(x\\=c\\(100\\.0\\)\\,y\\=mp\\[2\\,\\]\\,label\\=c\\(\\"100\\.0\\ \\%\\ \\(\\<\\=4\\.9e\\-324\\)\\"\\)\\,pos\\=4\\,offset\\=0\\.2\\,cex\\=0\\.9\\)\n+\\>\\ legend\\(\\"right\\"\\,legend\\=c\\(\\"Genome\\"\\,\\"ChIP\\ \\(p\\-value\\)\\"\\)\\,col\\=c\\(\\"\\#5FA1C1\\"\\,\\"\\#EB9D86\\"\\)\\,pch\\=15\\,bty\\=\\"n\\"\\)\n+\\>\\ \n+\\>\\ \\#\\ \n+\\>\\ \\#\\ Promoter\\,Bipromoter\\,Downstream\\,\\ Gene\\ and\\ Regions\\ of\\ interest\n+\\>\\ \\#\\ \n+\\>\\ \n+\\>\\ par\\(mfrow\\=c\\(4\\,\\ 1\\'..b'\\%\\"\\,\\"Intron\\:\\ 19\\.3\\ \\%\\"\\,\\"Distal\\ intergenic\\:\\ 67\\.0\\ \\%\\"\\)\\,col\\=c\\(\\"\\#445FA2\\"\\,\\"\\#EB9D86\\"\\,\\"\\#799F7A\\"\\,\\"\\#6C527F\\"\\,\\"\\#5FA1C1\\"\\,\\"\\#E8BB77\\"\\,\\"\\#A8C5EF\\"\\,\\"\\#FDCDB9\\"\\,\\"\\#C6E6B5\\"\\,\\"\\#F1D5EE\\"\\,\\"\\#B4E1F6\\"\\)\\,pch\\=15\\,bty\\=\\"n\\"\\)\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\\)\n+\\>\\ 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\\)\n+\\>\\ x\\<\\-c\\(0\\.000000\\,1\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,1\\.000000\\)\n+\\>\\ plot\\(x\\,\\ y\\,type\\=\\"n\\"\\,main\\=\\"\\"\\,xlab\\=\\"\\"\\,ylab\\=\\"\\"\\,frame\\=FALSE\\,axes\\=FALSE\\,xaxt\\=\\"s\\"\\,yaxt\\=\\"s\\"\\)\n+\\>\\ 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\\"\\)\n+\\>\\ \n+\\>\\ \\#\\ \n+\\>\\ \\#\\ ChIP\\ regions\\ over\\ the\\ genome\n+\\>\\ \\#\\ \n+\\>\\ \n+\\>\\ par\\(mar\\=c\\(4\\,\\ 4\\,\\ 5\\,\\ 3\\.8\\)\\,oma\\=c\\(4\\,\\ 2\\,\\ 4\\,\\ 2\\)\\)\n+\\>\\ layout\\(matrix\\(c\\(1\\,\\ 0\\,\\ 2\\,\\ 2\\)\\,\\ 2\\,\\ 2\\,\\ byrow\\ \\=\\ TRUE\\)\\,widths\\=c\\(1\\,\\ 1\\)\\,heights\\=c\\(1\\,\\ 5\\)\\)\n+\\>\\ x\\<\\-c\\(0\\.000000\\,2\\.515610\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,1\\.000000\\)\n+\\>\\ 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\\)\n+\\>\\ x\\<\\-c\\(0\\.000000\\,2\\.515610\\,2\\.515610\\,0\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,0\\.000000\\,1\\.000000\\,1\\.000000\\)\n+\\>\\ polygon\\(x\\,y\\,col\\=c\\(\\"black\\"\\)\\)\n+\\>\\ 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\\)\n+\\>\\ 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\\)\n+\\>\\ lines\\(x\\,\\ y\\,xlim\\=c\\(0\\,\\ 2\\.51561\\)\\,ylim\\=c\\(0\\,\\ 1\\)\\,type\\=\\"l\\"\\,col\\=c\\(\\"cyan\\"\\)\\,lwd\\=2\\)\n+\\>\\ x\\<\\-c\\(4119129\\.000000\\,4119130\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.855556\\,1\\.144444\\)\n+\\>\\ 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\\"\\)\n+\\>\\ start\\ \\<\\-\\ c\\(4119129\\)\n+\\>\\ end\\ \\<\\-\\ c\\(4119130\\)\n+\\>\\ vals\\ \\<\\-\\ c\\(2\\.51561\\)\n+\\>\\ vals\\[vals\\ \\>\\ 2\\.51561\\]\\ \\<\\-\\ 2\\.51561\n+\\>\\ vals\\[vals\\ \\<\\ 0\\]\\ \\<\\-\\ 0\n+\\>\\ heights\\ \\<\\-\\ 0\\.288889\\ \\*\\ \\(\\(vals\\ \\-\\ 0\\)\\/\\(2\\.51561\\ \\-\\ 0\\)\\)\\ \\+\\ 0\\.855555555556\n+\\>\\ for\\ \\(i\\ in\\ 1\\:length\\(heights\\)\\)\\ \\{\n+\\+\\ \\\tpolygon\\(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\\"\\)\\)\n+\\+\\ \\}\n+\\>\\ mtext\\(\\"26\\"\\,side\\=2\\,line\\=0\\,outer\\=FALSE\\,at\\=1\\.0\\)\n+\\>\\ dev\\.off\\(\\)\n+null\\ device\\ \n+\\ \\ \\ \\ \\ \\ \\ \\ \\ \\ 1\\ \n+\\>\\ \n+INFO\\ \\ \\@\\ .*\\ \\#\\.\\.\\.\\ cong\\!\\ See\\ ceas\\.pdf\\ for\\ the\\ graphical\\ results\\ of\\ CEAS\\!\\ \n' |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out1.pdf |
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| Binary file test-data/ceas_out1.pdf has changed |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out1.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ceas_out1.xls Tue Jun 30 07:08:05 2015 -0400 |
| b |
| b"@@ -0,0 +1,133 @@\n+# RefSeq: RefSeq ID\n+# chr: chromosome of a RefSeq gene\n+# txStart: 5' end of a RefSeq gene\n+# txEnd: 3' end site of a RefSeq gene\n+# strand: strand of a RefSeq gene\n+# dist u TSS: Distance to the nearest ChIP region's center upstream of transcription start site (bp)\n+# dist d TSS: Distance to the nearest ChIP region's center downstream of transcription start site (bp)\n+# dist u TTS: Distance to the nearest ChIP region's center upstream of transcription end site (bp)\n+# dist d TTS: Distance to the nearest ChIP region's center downstream of transcription end (bp)\n+# 3000bp u TSS: Occupancy rate of ChIP region in 3000bp upstream of transcription start site (0.0 - 1.0)\n+# 3000bp d TSS: Occupancy rate of ChIP region in 3000bp downstream of transcription start site (0.0 - 1.0)\n+# 1/3 gene: Occupancy rate of ChIP region in 1/3 gene (0.0 - 1.0)\n+# 2/3 gene: Occupancy rate of ChIP region in 2/3 gene (0.0 - 1.0)\n+# 3/3 gene: Occupancy rate of ChIP region in 3/3 gene (0.0 - 1.0)\n+# 3000bp d TTS: Occupancy rate of ChIP region in 3000bp downstream of transcriptino end (0.0 - 1.0)\n+# exons: Occupancy rate of ChIP regions in exons (0.0-1.0)\n+# 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.\n+#name\tchr\ttxStart\ttxEnd\tstrand\tdist u TSS\tdist d TSS\tdist u TTS\tdist d TTS\t3000bp u TSS\t3000bp d TSS\t1/3 gene\t2/3 gene\t3/3 gene\t3000bp d TTS\texons\n+NM_001031576\tchr26\t19281\t27136\t+\tNA\t4099848\tNA\t4091993\t0\t0\t0\t0\t0\t0\t0\n+NM_204615\tchr26\t57466\t61594\t-\t4057535\tNA\t4061663\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001005431\tchr26\t65800\t76175\t-\t4042954\tNA\t4053329\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001145491\tchr26\t91618\t92166\t-\t4026963\tNA\t4027511\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204398\tchr26\t93069\t97423\t+\tNA\t4026060\tNA\t4021706\t0\t0\t0\t0\t0\t0\t0\n+NM_001305147\tchr26\t254661\t282571\t+\tNA\t3864468\tNA\t3836558\t0\t0\t0\t0\t0\t0\t0\n+NM_001305148\tchr26\t254661\t282571\t+\tNA\t3864468\tNA\t3836558\t0\t0\t0\t0\t0\t0\t0\n+NM_001012868\tchr26\t350397\t355252\t-\t3763877\tNA\t3768732\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001031030\tchr26\t479573\t493561\t+\tNA\t3639556\tNA\t3625568\t0\t0\t0\t0\t0\t0\t0\n+NM_001305140\tchr26\t520705\t526012\t+\tNA\t3598424\tNA\t3593117\t0\t0\t0\t0\t0\t0\t0\n+NM_001031029\tchr26\t537101\t565572\t+\tNA\t3582028\tNA\t3553557\t0\t0\t0\t0\t0\t0\t0\n+NM_205248\tchr26\t537250\t760479\t+\tNA\t3581879\tNA\t3358650\t0\t0\t0\t0\t0\t0\t0\n+NM_204727\tchr26\t662969\t683066\t-\t3436063\tNA\t3456160\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_105475\tchr26\t669012\t669122\t-\t3450007\tNA\t3450117\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205449\tchr26\t785617\t794076\t+\tNA\t3333512\tNA\t3325053\t0\t0\t0\t0\t0\t0\t0\n+NM_204681\tchr26\t897458\t902049\t-\t3217080\tNA\t3221671\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001278156\tchr26\t905313\t917094\t-\t3202035\tNA\t3213816\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204184\tchr26\t960209\t964268\t-\t3154861\tNA\t3158920\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204316\tchr26\t974223\t991244\t+\tNA\t3144906\tNA\t3127885\t0\t0\t0\t0\t0\t0\t0\n+NM_001031028\tchr26\t993815\t1003847\t-\t3115282\tNA\t3125314\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006392\tchr26\t1024606\t1047756\t-\t3071373\tNA\t3094523\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001039596\tchr26\t1073550\t1080033\t-\t3039096\tNA\t3045579\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001031027\tchr26\t1090460\t1096137\t+\tNA\t3028669\tNA\t3022992\t0\t0\t0\t0\t0\t0\t0\n+NM_001031026\tchr26\t1096566\t1104751\t-\t3014378\tNA\t3022563\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030913\tchr26\t1122296\t1132596\t+\tNA\t2996833\tNA\t2986533\t0\t0\t0\t0\t0\t0\t0\n+NM_001171886\tchr26\t1220031\t1222791\t-\t2896338\tNA\t2899098\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205054\tchr26\t1229703\t1232833\t+\tNA\t2889426\tNA\t2886296\t0\t0\t0\t0\t0\t0\t0\n+NM_204462\tchr26\t1234686\t1236536\t-\t2882593\tNA\t2884443\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204463\tchr26\t1265724\t1267989\t-\t2851140\tNA\t2853405\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030378\tchr26\t1289091\t1290386\t-\t2828743\tNA\t2830038\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001195554\tchr26\t1382510\t1388447\t+\tNA\t2736619\tNA\t2730682\t0\t0\t0\t0\t0\t0\t0\n+NM_001012548\tchr26\t1406905\t1428443\t+\tNA\t2712224\tNA\t2690686\t0\t0\t0\t0\t0\t0\t0\n+NR_031486\tchr26\t1442696\t1442779\t-\t2676350\tNA\t2676433\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_031487\tchr26\t1442896\t1442979\t-\t2676150\tNA\t2676233\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205250\tchr26\t1472137\t1474003\t+\tNA\t2646992\tNA\t2645126\t0\t0\t0\t0\t0\t0\t0\n+NR_105486\tchr26\t1566398\t1566508\t-\t2552621\tNA"..b'4101\t0\t0\t0\t0\t0\t0\t0\n+NM_204664\tchr26\t2498398\t2509349\t+\tNA\t1620731\tNA\t1609780\t0\t0\t0\t0\t0\t0\t0\n+NR_031489\tchr26\t2511657\t2511746\t-\t1607383\tNA\t1607472\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_031490\tchr26\t2512568\t2512648\t-\t1606481\tNA\t1606561\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_105523\tchr26\t2669792\t2669902\t-\t1449227\tNA\t1449337\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_031491\tchr26\t2896046\t2896142\t+\tNA\t1223083\tNA\t1222987\t0\t0\t0\t0\t0\t0\t0\n+NM_001190924\tchr26\t2961382\t2962268\t+\tNA\t1157747\tNA\t1156861\t0\t0\t0\t0\t0\t0\t0\n+NM_001007881\tchr26\t2999189\t3002725\t+\tNA\t1119940\tNA\t1116404\t0\t0\t0\t0\t0\t0\t0\n+NM_204320\tchr26\t3006741\t3011817\t-\t1107312\tNA\t1112388\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030916\tchr26\t3035271\t3039335\t-\t1079794\tNA\t1083858\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204151\tchr26\t3047964\t3050306\t-\t1068823\tNA\t1071165\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204326\tchr26\t3124816\t3214381\t-\t904748\tNA\t994313\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204336\tchr26\t3320769\t3332327\t+\tNA\t798360\tNA\t786802\t0\t0\t0\t0\t0\t0\t0\n+NM_204622\tchr26\t3339753\t3358863\t-\t760266\tNA\t779376\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205515\tchr26\t3359016\t3368964\t+\tNA\t760113\tNA\t750165\t0\t0\t0\t0\t0\t0\t0\n+NM_001012843\tchr26\t3370712\t3377196\t+\tNA\t748417\tNA\t741933\t0\t0\t0\t0\t0\t0\t0\n+NM_001029849\tchr26\t3377655\t3382628\t-\t736501\tNA\t741474\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006323\tchr26\t3439841\t3454783\t-\t664346\tNA\t679288\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_035162\tchr26\t3455233\t3455324\t+\tNA\t663896\tNA\t663805\t0\t0\t0\t0\t0\t0\t0\n+NM_001012697\tchr26\t3516478\t3545774\t+\tNA\t602651\tNA\t573355\t0\t0\t0\t0\t0\t0\t0\n+NM_001030917\tchr26\t3590932\t3597509\t-\t521620\tNA\t528197\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001031500\tchr26\t3597231\t3600802\t+\tNA\t521898\tNA\t518327\t0\t0\t0\t0\t0\t0\t0\n+NM_001040018\tchr26\t3629575\t3631171\t+\tNA\t489554\tNA\t487958\t0\t0\t0\t0\t0\t0\t0\n+NM_001257295\tchr26\t3698350\t3701362\t-\t417767\tNA\t420779\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001257296\tchr26\t3701377\t3715857\t-\t403272\tNA\t417752\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001012549\tchr26\t3735643\t3742472\t-\t376657\tNA\t383486\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030918\tchr26\t3742618\t3760175\t-\t358954\tNA\t376511\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006324\tchr26\t3760758\t3765368\t-\t353761\tNA\t358371\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205063\tchr26\t3809805\t3812700\t+\tNA\t309324\tNA\t306429\t0\t0\t0\t0\t0\t0\t0\n+NM_001293109\tchr26\t3859074\t3879130\t-\t239999\tNA\t260055\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001293108\tchr26\t3859074\t3882051\t-\t237078\tNA\t260055\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_102328\tchr26\t3916006\t3918143\t-\t200986\tNA\t203123\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204728\tchr26\t3920817\t3937442\t-\t181687\tNA\t198312\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001244905\tchr26\t4104910\t4108376\t+\tNA\t14219\tNA\t10753\t0\t0\t0\t0\t0\t0\t0\n+NM_001293166\tchr26\t4138324\t4142325\t-\tNA\t23196\tNA\t19195\t0\t0\t0\t0\t0\t0\t0\n+NM_001030919\tchr26\t4144091\t4175943\t+\t24962\tNA\t56814\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001257297\tchr26\t4209891\t4216177\t+\t90762\tNA\t97048\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001257298\tchr26\t4218028\t4238067\t+\t98899\tNA\t118938\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205490\tchr26\t4375371\t4380959\t-\tNA\t261830\tNA\t256242\t0\t0\t0\t0\t0\t0\t0\n+NM_001305129\tchr26\t4391940\t4397490\t+\t272811\tNA\t278361\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001271612\tchr26\t4433568\t4438784\t+\t314439\tNA\t319655\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030920\tchr26\t4498991\t4730550\t+\t379862\tNA\t611421\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030921\tchr26\t4541748\t4544997\t-\tNA\t425868\tNA\t422619\t0\t0\t0\t0\t0\t0\t0\n+NM_001006325\tchr26\t4548211\t4559974\t+\t429082\tNA\t440845\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001037832\tchr26\t4571684\t4576072\t-\tNA\t456943\tNA\t452555\t0\t0\t0\t0\t0\t0\t0\n+NM_001080870\tchr26\t4578266\t4580646\t-\tNA\t461517\tNA\t459137\t0\t0\t0\t0\t0\t0\t0\n+NM_001080868\tchr26\t4578266\t4580647\t-\tNA\t461518\tNA\t459137\t0\t0\t0\t0\t0\t0\t0\n+NM_001030922\tchr26\t4730394\t4744364\t-\tNA\t625235\tNA\t611265\t0\t0\t0\t0\t0\t0\t0\n+NM_204877\tchr26\t4751619\t4755464\t-\tNA\t636335\tNA\t632490\t0\t0\t0\t0\t0\t0\t0\n+NM_001302134\tchr26\t4791084\t4792014\t+\t671955\tNA\t672885\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006327\tchr26\t4828534\t4833077\t-\tNA\t713948\tNA\t709405\t0\t0\t0\t0\t0\t0\t0\n+NM_001008453\tchr26\t4838545\t4850970\t-\tNA\t731841\tNA\t719416\t0\t0\t0\t0\t0\t0\t0\n+NM_001030923\tchr26\t4876559\t4884910\t+\t757430\tNA\t765781\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204429\tchr26\t4897094\t4901738\t-\tNA\t782609\tNA\t777965\t0\t0\t0\t0\t0\t0\t0\n+NM_204967\tchr26\t4946735\t4952662\t-\tNA\t833533\tNA\t827606\t0\t0\t0\t0\t0\t0\t0\n+NM_204473\tchr26\t4990765\t4993729\t+\t871636\tNA\t874600\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_105623\tchr26\t5087926\t5087980\t-\tNA\t968851\tNA\t968797\t0\t0\t0\t0\t0\t0\t0\n' |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ceas_out2.log Tue Jun 30 07:08:05 2015 -0400 |
| [ |
| b'@@ -0,0 +1,236 @@\n+ceas -- 0.9.9.7 (package version 1.0.2)\n+INFO @ Tue, 23 Jun 2015 11:24:09: \n+# ARGUMENTS: \n+# name = ceas\n+# gene annotation table = galGal3.refGene\n+# BED file = ceas_in.bed\n+# WIG file = ceas_in_stp1000.wig\n+# extra BED file = None\n+# ChIP annotation = On\n+# gene-centered annotation = On\n+# average profiling = On\n+# dump profiles = Off\n+# re-annotation for genome background (ChIP region annotation) = False\n+# promoter sizes (ChIP region annotation) = 1000,2000,3000 bp\n+# downstream sizes (ChIP region annotation) = 1000,2000,3000 bp\n+# bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp\n+# span size (gene-centered annotation) = 3000 bp\n+# profiling resolution (average profiling) = 50 bp\n+# relative distance wrt TSS and TTS (average profiling) = 3000 bp \n+INFO @ Tue, 23 Jun 2015 11:24:09: #1 read the gene table... \n+INFO @ Tue, 23 Jun 2015 11:24:09: #2 read the bed file of ChIP regions... \n+INFO @ Tue, 23 Jun 2015 11:24:09: #3 perform gene-centered annotation... \n+INFO @ Tue, 23 Jun 2015 11:24:09: #4 See ceas.xls for gene-centered annotation! \n+INFO @ Tue, 23 Jun 2015 11:24:09: #5 read the pre-computed genome bg annotation... \n+INFO @ Tue, 23 Jun 2015 11:24:09: #6 perform ChIP region annotation... \n+INFO @ Tue, 23 Jun 2015 11:24:09: #7 write a R script of ChIP region annotation... \n+INFO @ Tue, 23 Jun 2015 11:24:09: #8-1 run wig profiling of chr26... \n+INFO @ Tue, 23 Jun 2015 11:24:09: #9 append an R script of wig profiling... \n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-redhat-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> # ARGUMENTS: \n+> # name = ceas\n+> # gene annotation table = galGal3.refGene\n+> # BED file = ceas_in.bed\n+> # WIG file = ceas_in_stp1000.wig\n+> # extra BED file = None\n+> # ChIP annotation = On\n+> # gene-centered annotation = On\n+> # average profiling = On\n+> # dump profiles = Off\n+> # re-annotation for genome background (ChIP region annotation) = False\n+> # promoter sizes (ChIP region annotation) = 1000,2000,3000 bp\n+> # downstream sizes (ChIP region annotation) = 1000,2000,3000 bp\n+> # bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp\n+> # span size (gene-centered annotation) = 3000 bp\n+> # profiling resolution (average profiling) = 50 bp\n+> # relative distance wrt TSS and TTS (average profiling) = 3000 bp\n+> pdf("ceas.pdf",height=11.5,width=8.5)\n+> \n+> # 11:24:09 Tue, 23 Jun 2015\n+> # \n+> # ChIP annotation\n+> # \n+> \n+> \n+> # \n+> # Chromosomal Distribution\n+> # \n+> \n+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))\n+> r0<-c(100.0)\n+> r1<-c(100.0)\n+> height<-rbind(r0,r1)\n+> names=c("26")\n+> 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)\n+> text(x=c(100.0),y=mp[1,],label=c("100.0 %"),pos=4,offset=0.2,cex=0.9)\n+> text(x=c(100.0),y=mp[2,],label=c("100.0 % (<=4.9e-324)"),pos=4,offset=0.2,cex=0.9)\n+> legend("right",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")\n+> \n+> # \n+> # Promoter,Bipromoter,Downstream, Gene and Regions of interest\n+> # \n+> \n+> par(mfrow=c(4, 1),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))\n+> r0<-c(1.8532425688606797, 3.616851183410451, 5.322318854623416)\n+> r1<-c(0.0, 0.0, 0.0)\n+> height<-rbind(r0,r1)\n+> names=c("<=1000 '..b'ack"))\n+> 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)\n+> 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)\n+> 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)\n+> 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)\n+> 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)\n+> 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)\n+> par(mfrow=c(3, 2),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))\n+> x<-c(0.000000,50.000000,100.000000)\n+> y<-c(0.000000,0.000000,0.000000)\n+> plot(x, y,type="l",main="Average Exon Profile\n++ (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)\n+> x<-c(0.000000,25.000000,50.000000,75.000000,100.000000)\n+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000)\n+> plot(x, y,type="l",main="Average Intron Profile\n++ (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)\n+> x<-c(0.000000,50.000000,100.000000)\n+> y<-c(0.000000,0.000000,0.000000)\n+> plot(x, y,type="l",main="Average Exon Profile\n++ (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)\n+> x<-c(0.000000,11.111111,22.222222,33.333333,44.444444,55.555556,66.666667,77.777778,88.888889,100.000000)\n+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)\n+> plot(x, y,type="l",main="Average Intron Profile\n++ (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)\n+> x<-c(0.000000,33.333333,66.666667,100.000000)\n+> y<-c(0.000000,0.000000,0.000000,0.000000)\n+> plot(x, y,type="l",main="Average Exon Profile\n++ (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)\n+> 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)\n+> 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)\n+> plot(x, y,type="l",main="Average Intron Profile\n++ (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)\n+> dev.off()\n+null device \n+ 1 \n+> \n+INFO @ Tue, 23 Jun 2015 11:24:09: #... cong! See ceas.pdf for the graphical results of CEAS! \n' |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out2.log.re_match --- /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 |
| [ |
| b'@@ -0,0 +1,236 @@\n+ceas\\ \\-\\-\\ 0\\.9\\.9\\.7\\ \\(package\\ version\\ 1\\.0\\.2\\)\n+INFO\\ \\ \\@\\ .* \n+\\#\\ ARGUMENTS\\:\\ \n+\\#\\ name\\ \\=\\ ceas\n+\\#\\ gene\\ annotation\\ table\\ \\=\\ .*galGal3\\.refGene\n+\\#\\ BED\\ file\\ \\=\\ .*\n+\\#\\ WIG\\ file\\ \\=\\ .*\n+\\#\\ extra\\ BED\\ file\\ \\=\\ None\n+\\#\\ ChIP\\ annotation\\ \\=\\ On\n+\\#\\ gene\\-centered\\ annotation\\ \\=\\ \\ On\n+\\#\\ average\\ profiling\\ \\=\\ On\n+\\#\\ dump\\ profiles\\ \\=\\ Off\n+\\#\\ re\\-annotation\\ for\\ genome\\ background\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ False\n+\\#\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\#\\ downstream\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\#\\ bidrectional\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 2500\\,5000\\ bp\n+\\#\\ span\\ size\\ \\(gene\\-centered\\ annotation\\)\\ \\=\\ 3000\\ bp\n+\\#\\ profiling\\ resolution\\ \\(average\\ profiling\\)\\ \\=\\ 50\\ bp\n+\\#\\ relative\\ distance\\ wrt\\ TSS\\ and\\ TTS\\ \\(average\\ profiling\\)\\ \\=\\ 3000\\ bp\\ \n+INFO\\ \\ \\@\\ .*\\ \\#1\\ read\\ the\\ gene\\ table\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#2\\ read\\ the\\ bed\\ file\\ of\\ ChIP\\ regions\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#3\\ perform\\ gene\\-centered\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#4\\ See\\ ceas\\.xls\\ for\\ gene\\-centered\\ annotation\\!\\ \n+INFO\\ \\ \\@\\ .*\\ \\#5\\ read\\ the\\ pre\\-computed\\ genome\\ bg\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#6\\ perform\\ ChIP\\ region\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#7\\ write\\ a\\ R\\ script\\ of\\ ChIP\\ region\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#8\\-1\\ run\\ wig\\ profiling\\ of\\ chr26\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#9\\ append\\ an\\ R\\ script\\ of\\ wig\\ profiling\\.\\.\\.\\ \n+\n+R\\ version\\ 3\\.1\\.2\\ \\(2014\\-10\\-31\\)\\ \\-\\-\\ \\"Pumpkin\\ Helmet\\"\n+Copyright\\ \\(C\\)\\ 2014\\ The\\ R\\ Foundation\\ for\\ Statistical\\ Computing\n+Platform\\:\\ .*\n+\n+R\\ is\\ free\\ software\\ and\\ comes\\ with\\ ABSOLUTELY\\ NO\\ WARRANTY\\.\n+You\\ are\\ welcome\\ to\\ redistribute\\ it\\ under\\ certain\\ conditions\\.\n+Type\\ \\\'license\\(\\)\\\'\\ or\\ \\\'licence\\(\\)\\\'\\ for\\ distribution\\ details\\.\n+\n+\\ \\ Natural\\ language\\ support\\ but\\ running\\ in\\ an\\ English\\ locale\n+\n+R\\ is\\ a\\ collaborative\\ project\\ with\\ many\\ contributors\\.\n+Type\\ \\\'contributors\\(\\)\\\'\\ for\\ more\\ information\\ and\n+\\\'citation\\(\\)\\\'\\ on\\ how\\ to\\ cite\\ R\\ or\\ R\\ packages\\ in\\ publications\\.\n+\n+Type\\ \\\'demo\\(\\)\\\'\\ for\\ some\\ demos\\,\\ \\\'help\\(\\)\\\'\\ for\\ on\\-line\\ help\\,\\ or\n+\\\'help\\.start\\(\\)\\\'\\ for\\ an\\ HTML\\ browser\\ interface\\ to\\ help\\.\n+Type\\ \\\'q\\(\\)\\\'\\ to\\ quit\\ R\\.\n+\n+\\>\\ \\#\\ ARGUMENTS\\:\\ \n+\\>\\ \\#\\ name\\ \\=\\ ceas\n+\\>\\ \\#\\ gene\\ annotation\\ table\\ \\=\\ .*galGal3\\.refGene\n+\\>\\ \\#\\ BED\\ file\\ \\=\\ .*\n+\\>\\ \\#\\ WIG\\ file\\ \\=\\ .*\n+\\>\\ \\#\\ extra\\ BED\\ file\\ \\=\\ None\n+\\>\\ \\#\\ ChIP\\ annotation\\ \\=\\ On\n+\\>\\ \\#\\ gene\\-centered\\ annotation\\ \\=\\ \\ On\n+\\>\\ \\#\\ average\\ profiling\\ \\=\\ On\n+\\>\\ \\#\\ dump\\ profiles\\ \\=\\ Off\n+\\>\\ \\#\\ re\\-annotation\\ for\\ genome\\ background\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ False\n+\\>\\ \\#\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\>\\ \\#\\ downstream\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\>\\ \\#\\ bidrectional\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 2500\\,5000\\ bp\n+\\>\\ \\#\\ span\\ size\\ \\(gene\\-centered\\ annotation\\)\\ \\=\\ 3000\\ bp\n+\\>\\ \\#\\ profiling\\ resolution\\ \\(average\\ profiling\\)\\ \\=\\ 50\\ bp\n+\\>\\ \\#\\ relative\\ distance\\ wrt\\ TSS\\ and\\ TTS\\ \\(average\\ profiling\\)\\ \\=\\ 3000\\ bp\n+\\>\\ pdf\\(\\"ceas\\.pdf\\"\\,height\\=11\\.5\\,width\\=8\\.5\\)\n+\\>\\ \n+\\>\\ \\#\\ .*\n+\\>\\ \\#\\ \n+\\>\\ \\#\\ ChIP\\ annotation\n+\\>\\ \\#\\ \n+\\>\\ \n+\\>\\ \n+\\>\\ \\#\\ \n+\\>\\ \\#\\ Chromosomal\\ Distribution\n+\\>\\ \\#\\ \n+\\>\\ \n+\\>\\ par\\(mar\\=c\\(4\\,\\ 4\\,\\ 5\\,\\ 3\\.8\\)\\,oma\\=c\\(4\\,\\ 2\\,\\ 4\\,\\ 2\\)\\)\n+\\>\\ r0\\<\\-c\\(100\\.0\\)\n+\\>\\ r1\\<\\-c\\(100\\.0\\)\n+\\>\\ height\\<\\-rbind\\(r0\\,r1\\)\n+\\>\\ names\\=c\\(\\"26\\"\\)\n+\\>\\ 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\\)\n+\\>\\ text\\(x\\=c\\(100\\.0\\)\\,y\\=mp\\[1\\,\\]\\,label\\=c\\(\\"100\\.0\\ \\%\\"\\)'..b'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\\)\n+\\>\\ 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\\)\n+\\>\\ 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\\)\n+\\>\\ par\\(mfrow\\=c\\(3\\,\\ 2\\)\\,mar\\=c\\(4\\,\\ 4\\,\\ 5\\,\\ 3\\.8\\)\\,oma\\=c\\(4\\,\\ 2\\,\\ 4\\,\\ 2\\)\\)\n+\\>\\ x\\<\\-c\\(0\\.000000\\,50\\.000000\\,100\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,0\\.000000\\,0\\.000000\\)\n+\\>\\ plot\\(x\\,\\ y\\,type\\=\\"l\\"\\,main\\=\\"Average\\ Exon\\ Profile\n+\\+\\ \\(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\\)\n+\\>\\ x\\<\\-c\\(0\\.000000\\,25\\.000000\\,50\\.000000\\,75\\.000000\\,100\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\)\n+\\>\\ plot\\(x\\,\\ y\\,type\\=\\"l\\"\\,main\\=\\"Average\\ Intron\\ Profile\n+\\+\\ \\(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\\)\n+\\>\\ x\\<\\-c\\(0\\.000000\\,50\\.000000\\,100\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,0\\.000000\\,0\\.000000\\)\n+\\>\\ plot\\(x\\,\\ y\\,type\\=\\"l\\"\\,main\\=\\"Average\\ Exon\\ Profile\n+\\+\\ \\(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\\)\n+\\>\\ x\\<\\-c\\(0\\.000000\\,11\\.111111\\,22\\.222222\\,33\\.333333\\,44\\.444444\\,55\\.555556\\,66\\.666667\\,77\\.777778\\,88\\.888889\\,100\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\)\n+\\>\\ plot\\(x\\,\\ y\\,type\\=\\"l\\"\\,main\\=\\"Average\\ Intron\\ Profile\n+\\+\\ \\(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\\)\n+\\>\\ x\\<\\-c\\(0\\.000000\\,33\\.333333\\,66\\.666667\\,100\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,0\\.000000\\,0\\.000000\\,0\\.000000\\)\n+\\>\\ plot\\(x\\,\\ y\\,type\\=\\"l\\"\\,main\\=\\"Average\\ Exon\\ Profile\n+\\+\\ \\(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\\)\n+\\>\\ 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\\)\n+\\>\\ 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\\)\n+\\>\\ plot\\(x\\,\\ y\\,type\\=\\"l\\"\\,main\\=\\"Average\\ Intron\\ Profile\n+\\+\\ \\(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\\)\n+\\>\\ dev\\.off\\(\\)\n+null\\ device\\ \n+\\ \\ \\ \\ \\ \\ \\ \\ \\ \\ 1\\ \n+\\>\\ \n+INFO\\ \\ \\@\\ .*\\ \\#\\.\\.\\.\\ cong\\!\\ See\\ ceas\\.pdf\\ for\\ the\\ graphical\\ results\\ of\\ CEAS\\!\\ \n' |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out2.pdf |
| b |
| Binary file test-data/ceas_out2.pdf has changed |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out2.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ceas_out2.xls Tue Jun 30 07:08:05 2015 -0400 |
| b |
| b"@@ -0,0 +1,133 @@\n+# RefSeq: RefSeq ID\n+# chr: chromosome of a RefSeq gene\n+# txStart: 5' end of a RefSeq gene\n+# txEnd: 3' end site of a RefSeq gene\n+# strand: strand of a RefSeq gene\n+# dist u TSS: Distance to the nearest ChIP region's center upstream of transcription start site (bp)\n+# dist d TSS: Distance to the nearest ChIP region's center downstream of transcription start site (bp)\n+# dist u TTS: Distance to the nearest ChIP region's center upstream of transcription end site (bp)\n+# dist d TTS: Distance to the nearest ChIP region's center downstream of transcription end (bp)\n+# 3000bp u TSS: Occupancy rate of ChIP region in 3000bp upstream of transcription start site (0.0 - 1.0)\n+# 3000bp d TSS: Occupancy rate of ChIP region in 3000bp downstream of transcription start site (0.0 - 1.0)\n+# 1/3 gene: Occupancy rate of ChIP region in 1/3 gene (0.0 - 1.0)\n+# 2/3 gene: Occupancy rate of ChIP region in 2/3 gene (0.0 - 1.0)\n+# 3/3 gene: Occupancy rate of ChIP region in 3/3 gene (0.0 - 1.0)\n+# 3000bp d TTS: Occupancy rate of ChIP region in 3000bp downstream of transcriptino end (0.0 - 1.0)\n+# exons: Occupancy rate of ChIP regions in exons (0.0-1.0)\n+# 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.\n+#name\tchr\ttxStart\ttxEnd\tstrand\tdist u TSS\tdist d TSS\tdist u TTS\tdist d TTS\t3000bp u TSS\t3000bp d TSS\t1/3 gene\t2/3 gene\t3/3 gene\t3000bp d TTS\texons\n+NM_001031576\tchr26\t19281\t27136\t+\tNA\t4099848\tNA\t4091993\t0\t0\t0\t0\t0\t0\t0\n+NM_204615\tchr26\t57466\t61594\t-\t4057535\tNA\t4061663\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001005431\tchr26\t65800\t76175\t-\t4042954\tNA\t4053329\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001145491\tchr26\t91618\t92166\t-\t4026963\tNA\t4027511\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204398\tchr26\t93069\t97423\t+\tNA\t4026060\tNA\t4021706\t0\t0\t0\t0\t0\t0\t0\n+NM_001305147\tchr26\t254661\t282571\t+\tNA\t3864468\tNA\t3836558\t0\t0\t0\t0\t0\t0\t0\n+NM_001305148\tchr26\t254661\t282571\t+\tNA\t3864468\tNA\t3836558\t0\t0\t0\t0\t0\t0\t0\n+NM_001012868\tchr26\t350397\t355252\t-\t3763877\tNA\t3768732\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001031030\tchr26\t479573\t493561\t+\tNA\t3639556\tNA\t3625568\t0\t0\t0\t0\t0\t0\t0\n+NM_001305140\tchr26\t520705\t526012\t+\tNA\t3598424\tNA\t3593117\t0\t0\t0\t0\t0\t0\t0\n+NM_001031029\tchr26\t537101\t565572\t+\tNA\t3582028\tNA\t3553557\t0\t0\t0\t0\t0\t0\t0\n+NM_205248\tchr26\t537250\t760479\t+\tNA\t3581879\tNA\t3358650\t0\t0\t0\t0\t0\t0\t0\n+NM_204727\tchr26\t662969\t683066\t-\t3436063\tNA\t3456160\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_105475\tchr26\t669012\t669122\t-\t3450007\tNA\t3450117\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205449\tchr26\t785617\t794076\t+\tNA\t3333512\tNA\t3325053\t0\t0\t0\t0\t0\t0\t0\n+NM_204681\tchr26\t897458\t902049\t-\t3217080\tNA\t3221671\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001278156\tchr26\t905313\t917094\t-\t3202035\tNA\t3213816\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204184\tchr26\t960209\t964268\t-\t3154861\tNA\t3158920\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204316\tchr26\t974223\t991244\t+\tNA\t3144906\tNA\t3127885\t0\t0\t0\t0\t0\t0\t0\n+NM_001031028\tchr26\t993815\t1003847\t-\t3115282\tNA\t3125314\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006392\tchr26\t1024606\t1047756\t-\t3071373\tNA\t3094523\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001039596\tchr26\t1073550\t1080033\t-\t3039096\tNA\t3045579\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001031027\tchr26\t1090460\t1096137\t+\tNA\t3028669\tNA\t3022992\t0\t0\t0\t0\t0\t0\t0\n+NM_001031026\tchr26\t1096566\t1104751\t-\t3014378\tNA\t3022563\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030913\tchr26\t1122296\t1132596\t+\tNA\t2996833\tNA\t2986533\t0\t0\t0\t0\t0\t0\t0\n+NM_001171886\tchr26\t1220031\t1222791\t-\t2896338\tNA\t2899098\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205054\tchr26\t1229703\t1232833\t+\tNA\t2889426\tNA\t2886296\t0\t0\t0\t0\t0\t0\t0\n+NM_204462\tchr26\t1234686\t1236536\t-\t2882593\tNA\t2884443\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204463\tchr26\t1265724\t1267989\t-\t2851140\tNA\t2853405\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030378\tchr26\t1289091\t1290386\t-\t2828743\tNA\t2830038\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001195554\tchr26\t1382510\t1388447\t+\tNA\t2736619\tNA\t2730682\t0\t0\t0\t0\t0\t0\t0\n+NM_001012548\tchr26\t1406905\t1428443\t+\tNA\t2712224\tNA\t2690686\t0\t0\t0\t0\t0\t0\t0\n+NR_031486\tchr26\t1442696\t1442779\t-\t2676350\tNA\t2676433\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_031487\tchr26\t1442896\t1442979\t-\t2676150\tNA\t2676233\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205250\tchr26\t1472137\t1474003\t+\tNA\t2646992\tNA\t2645126\t0\t0\t0\t0\t0\t0\t0\n+NR_105486\tchr26\t1566398\t1566508\t-\t2552621\tNA"..b'4101\t0\t0\t0\t0\t0\t0\t0\n+NM_204664\tchr26\t2498398\t2509349\t+\tNA\t1620731\tNA\t1609780\t0\t0\t0\t0\t0\t0\t0\n+NR_031489\tchr26\t2511657\t2511746\t-\t1607383\tNA\t1607472\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_031490\tchr26\t2512568\t2512648\t-\t1606481\tNA\t1606561\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_105523\tchr26\t2669792\t2669902\t-\t1449227\tNA\t1449337\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_031491\tchr26\t2896046\t2896142\t+\tNA\t1223083\tNA\t1222987\t0\t0\t0\t0\t0\t0\t0\n+NM_001190924\tchr26\t2961382\t2962268\t+\tNA\t1157747\tNA\t1156861\t0\t0\t0\t0\t0\t0\t0\n+NM_001007881\tchr26\t2999189\t3002725\t+\tNA\t1119940\tNA\t1116404\t0\t0\t0\t0\t0\t0\t0\n+NM_204320\tchr26\t3006741\t3011817\t-\t1107312\tNA\t1112388\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030916\tchr26\t3035271\t3039335\t-\t1079794\tNA\t1083858\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204151\tchr26\t3047964\t3050306\t-\t1068823\tNA\t1071165\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204326\tchr26\t3124816\t3214381\t-\t904748\tNA\t994313\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204336\tchr26\t3320769\t3332327\t+\tNA\t798360\tNA\t786802\t0\t0\t0\t0\t0\t0\t0\n+NM_204622\tchr26\t3339753\t3358863\t-\t760266\tNA\t779376\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205515\tchr26\t3359016\t3368964\t+\tNA\t760113\tNA\t750165\t0\t0\t0\t0\t0\t0\t0\n+NM_001012843\tchr26\t3370712\t3377196\t+\tNA\t748417\tNA\t741933\t0\t0\t0\t0\t0\t0\t0\n+NM_001029849\tchr26\t3377655\t3382628\t-\t736501\tNA\t741474\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006323\tchr26\t3439841\t3454783\t-\t664346\tNA\t679288\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_035162\tchr26\t3455233\t3455324\t+\tNA\t663896\tNA\t663805\t0\t0\t0\t0\t0\t0\t0\n+NM_001012697\tchr26\t3516478\t3545774\t+\tNA\t602651\tNA\t573355\t0\t0\t0\t0\t0\t0\t0\n+NM_001030917\tchr26\t3590932\t3597509\t-\t521620\tNA\t528197\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001031500\tchr26\t3597231\t3600802\t+\tNA\t521898\tNA\t518327\t0\t0\t0\t0\t0\t0\t0\n+NM_001040018\tchr26\t3629575\t3631171\t+\tNA\t489554\tNA\t487958\t0\t0\t0\t0\t0\t0\t0\n+NM_001257295\tchr26\t3698350\t3701362\t-\t417767\tNA\t420779\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001257296\tchr26\t3701377\t3715857\t-\t403272\tNA\t417752\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001012549\tchr26\t3735643\t3742472\t-\t376657\tNA\t383486\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030918\tchr26\t3742618\t3760175\t-\t358954\tNA\t376511\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006324\tchr26\t3760758\t3765368\t-\t353761\tNA\t358371\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205063\tchr26\t3809805\t3812700\t+\tNA\t309324\tNA\t306429\t0\t0\t0\t0\t0\t0\t0\n+NM_001293109\tchr26\t3859074\t3879130\t-\t239999\tNA\t260055\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001293108\tchr26\t3859074\t3882051\t-\t237078\tNA\t260055\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_102328\tchr26\t3916006\t3918143\t-\t200986\tNA\t203123\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204728\tchr26\t3920817\t3937442\t-\t181687\tNA\t198312\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001244905\tchr26\t4104910\t4108376\t+\tNA\t14219\tNA\t10753\t0\t0\t0\t0\t0\t0\t0\n+NM_001293166\tchr26\t4138324\t4142325\t-\tNA\t23196\tNA\t19195\t0\t0\t0\t0\t0\t0\t0\n+NM_001030919\tchr26\t4144091\t4175943\t+\t24962\tNA\t56814\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001257297\tchr26\t4209891\t4216177\t+\t90762\tNA\t97048\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001257298\tchr26\t4218028\t4238067\t+\t98899\tNA\t118938\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205490\tchr26\t4375371\t4380959\t-\tNA\t261830\tNA\t256242\t0\t0\t0\t0\t0\t0\t0\n+NM_001305129\tchr26\t4391940\t4397490\t+\t272811\tNA\t278361\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001271612\tchr26\t4433568\t4438784\t+\t314439\tNA\t319655\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030920\tchr26\t4498991\t4730550\t+\t379862\tNA\t611421\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030921\tchr26\t4541748\t4544997\t-\tNA\t425868\tNA\t422619\t0\t0\t0\t0\t0\t0\t0\n+NM_001006325\tchr26\t4548211\t4559974\t+\t429082\tNA\t440845\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001037832\tchr26\t4571684\t4576072\t-\tNA\t456943\tNA\t452555\t0\t0\t0\t0\t0\t0\t0\n+NM_001080870\tchr26\t4578266\t4580646\t-\tNA\t461517\tNA\t459137\t0\t0\t0\t0\t0\t0\t0\n+NM_001080868\tchr26\t4578266\t4580647\t-\tNA\t461518\tNA\t459137\t0\t0\t0\t0\t0\t0\t0\n+NM_001030922\tchr26\t4730394\t4744364\t-\tNA\t625235\tNA\t611265\t0\t0\t0\t0\t0\t0\t0\n+NM_204877\tchr26\t4751619\t4755464\t-\tNA\t636335\tNA\t632490\t0\t0\t0\t0\t0\t0\t0\n+NM_001302134\tchr26\t4791084\t4792014\t+\t671955\tNA\t672885\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006327\tchr26\t4828534\t4833077\t-\tNA\t713948\tNA\t709405\t0\t0\t0\t0\t0\t0\t0\n+NM_001008453\tchr26\t4838545\t4850970\t-\tNA\t731841\tNA\t719416\t0\t0\t0\t0\t0\t0\t0\n+NM_001030923\tchr26\t4876559\t4884910\t+\t757430\tNA\t765781\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204429\tchr26\t4897094\t4901738\t-\tNA\t782609\tNA\t777965\t0\t0\t0\t0\t0\t0\t0\n+NM_204967\tchr26\t4946735\t4952662\t-\tNA\t833533\tNA\t827606\t0\t0\t0\t0\t0\t0\t0\n+NM_204473\tchr26\t4990765\t4993729\t+\t871636\tNA\t874600\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_105623\tchr26\t5087926\t5087980\t-\tNA\t968851\tNA\t968797\t0\t0\t0\t0\t0\t0\t0\n' |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out3.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ceas_out3.log Tue Jun 30 07:08:05 2015 -0400 |
| b |
| b'@@ -0,0 +1,235 @@\n+/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).\n+ warnings.warn(msg, UserWarning)\n+ceasBW -- 0.9.9.7 (package version 1.0.2)\n+/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).\n+ warnings.warn(msg, UserWarning)\n+INFO @ Tue, 23 Jun 2015 13:03:32: \n+# ARGUMENTS: \n+# name = ceas\n+# gene annotation table = galGal3.refGene\n+# BED file = ceas_in.bed\n+# WIG file = ceas_in.bigwig\n+# extra BED file = None\n+# ChIP annotation = On\n+# gene-centered annotation = On\n+# average profiling = On\n+# dump profiles = Off\n+# re-annotation for genome background (ChIP region annotation) = False\n+# promoter sizes (ChIP region annotation) = 1000,2000,3000 bp\n+# downstream sizes (ChIP region annotation) = 1000,2000,3000 bp\n+# bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp\n+# span size (gene-centered annotation) = 3000 bp\n+# profiling resolution (average profiling) = 50 bp\n+# relative distance wrt TSS and TTS (average profiling) = 3000 bp \n+INFO @ Tue, 23 Jun 2015 13:03:32: #1 read the gene table... \n+INFO @ Tue, 23 Jun 2015 13:03:32: #2 read the bed file of ChIP regions... \n+INFO @ Tue, 23 Jun 2015 13:03:32: #3 perform gene-centered annotation... \n+INFO @ Tue, 23 Jun 2015 13:03:32: #4 See ceas.xls for gene-centered annotation! \n+INFO @ Tue, 23 Jun 2015 13:03:32: #5 read the pre-computed genome bg annotation... \n+INFO @ Tue, 23 Jun 2015 13:03:32: #6 perform ChIP region annotation... \n+INFO @ Tue, 23 Jun 2015 13:03:32: #7 write a R script of ChIP region annotation... \n+INFO @ Tue, 23 Jun 2015 13:03:32: #8-1 run wig profiling of chr26... \n+INFO @ Tue, 23 Jun 2015 13:03:32: #9 append an R script of wig profiling... \n+\n+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"\n+Copyright (C) 2014 The R Foundation for Statistical Computing\n+Platform: x86_64-redhat-linux-gnu (64-bit)\n+\n+R is free software and comes with ABSOLUTELY NO WARRANTY.\n+You are welcome to redistribute it under certain conditions.\n+Type \'license()\' or \'licence()\' for distribution details.\n+\n+ Natural language support but running in an English locale\n+\n+R is a collaborative project with many contributors.\n+Type \'contributors()\' for more information and\n+\'citation()\' on how to cite R or R packages in publications.\n+\n+Type \'demo()\' for some demos, \'help()\' for on-line help, or\n+\'help.start()\' for an HTML browser interface to help.\n+Type \'q()\' to quit R.\n+\n+> # ARGUMENTS: \n+> # name = ceas\n+> # gene annotation table = galGal3.refGene\n+> # BED file = ceas_in.bed\n+> # WIG file = ceas_in.bigwig\n+> # extra BED file = None\n+> # ChIP annotation = On\n+> # gene-centered annotation = On\n+> # average profiling = On\n+> # dump profiles = Off\n+> # re-annotation for genome background (ChIP region annotation) = False\n+> # promoter sizes (ChIP region annotation) = 1000,2000,3000 bp\n+> # downstream sizes (ChIP region annotation) = 1000,2000,3000 bp\n+> # bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp\n+> # span size (gene-centered annotation) = 3000 bp\n+> # profiling resolution (average profiling) = 50 bp\n+> # relative distance wrt TSS and TTS (average profiling) = 3000 bp\n+> pdf("ceas.pdf",height=11.5,width=8.5)\n+> \n+> # 13:03:32 Tue, 23 Jun 2015\n+> # \n+> # ChIP annotation\n+> # \n+> \n+> \n+> # \n+> # Chromosomal Distribution\n+> # \n+> \n+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))\n+> r0<-c(100.0)\n+> r1<-c(100.0)\n+> height<-rbind(r0,r1)\n'..b'.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)\n+> 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)\n+> abline(v=0.000000,lty=2,col=c("black"))\n+> abline(v=3000.000000,lty=2,col=c("black"))\n+> 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)\n+> 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)\n+> 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)\n+> 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)\n+> 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)\n+> 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)\n+> par(mfrow=c(3, 2),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))\n+> x<-c(-3.000000,3.000000)\n+> y<-c(0.000000,1.000000)\n+> 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")\n+> x<-c(-3.000000,3.000000)\n+> y<-c(0.000000,1.000000)\n+> 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")\n+> x<-c(-3.000000,3.000000)\n+> y<-c(0.000000,1.000000)\n+> 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")\n+> x<-c(-3.000000,3.000000)\n+> y<-c(0.000000,1.000000)\n+> 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")\n+> x<-c(-3.000000,3.000000)\n+> y<-c(0.000000,1.000000)\n+> 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")\n+> 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)\n+> 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)\n+> plot(x, y,type="l",main="Average Intron Profile\n++ (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)\n+> dev.off()\n+null device \n+ 1 \n+> \n+INFO @ Tue, 23 Jun 2015 13:03:33: #... cong! See ceas.pdf for the graphical results of CEAS! \n' |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out3.log.re_match --- /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 |
| [ |
| b'@@ -0,0 +1,231 @@\n+ceasBW\\ \\-\\-\\ 0\\.9\\.9\\.7\\ \\(package\\ version\\ 1\\.0\\.2\\)\n+INFO\\ \\ \\@\\ .*\\ \n+\\#\\ ARGUMENTS\\:\\ \n+\\#\\ name\\ \\=\\ ceas\n+\\#\\ gene\\ annotation\\ table\\ \\=\\ .*galGal3\\.refGene\n+\\#\\ BED\\ file\\ \\=\\ .*\n+\\#\\ WIG\\ file\\ \\=\\ .*\n+\\#\\ extra\\ BED\\ file\\ \\=\\ None\n+\\#\\ ChIP\\ annotation\\ \\=\\ On\n+\\#\\ gene\\-centered\\ annotation\\ \\=\\ \\ On\n+\\#\\ average\\ profiling\\ \\=\\ On\n+\\#\\ dump\\ profiles\\ \\=\\ Off\n+\\#\\ re\\-annotation\\ for\\ genome\\ background\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ False\n+\\#\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\#\\ downstream\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\#\\ bidrectional\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 2500\\,5000\\ bp\n+\\#\\ span\\ size\\ \\(gene\\-centered\\ annotation\\)\\ \\=\\ 3000\\ bp\n+\\#\\ profiling\\ resolution\\ \\(average\\ profiling\\)\\ \\=\\ 50\\ bp\n+\\#\\ relative\\ distance\\ wrt\\ TSS\\ and\\ TTS\\ \\(average\\ profiling\\)\\ \\=\\ 3000\\ bp\\ \n+INFO\\ \\ \\@\\ .*\\ \\#1\\ read\\ the\\ gene\\ table\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#2\\ read\\ the\\ bed\\ file\\ of\\ ChIP\\ regions\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#3\\ perform\\ gene\\-centered\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#4\\ See\\ ceas\\.xls\\ for\\ gene\\-centered\\ annotation\\!\\ \n+INFO\\ \\ \\@\\ .*\\ \\#5\\ read\\ the\\ pre\\-computed\\ genome\\ bg\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#6\\ perform\\ ChIP\\ region\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#7\\ write\\ a\\ R\\ script\\ of\\ ChIP\\ region\\ annotation\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#8\\-1\\ run\\ wig\\ profiling\\ of\\ chr26\\.\\.\\.\\ \n+INFO\\ \\ \\@\\ .*\\ \\#9\\ append\\ an\\ R\\ script\\ of\\ wig\\ profiling\\.\\.\\.\\ \n+\n+R\\ version\\ 3\\.1\\.2\\ \\(2014\\-10\\-31\\)\\ \\-\\-\\ \\"Pumpkin\\ Helmet\\"\n+Copyright\\ \\(C\\)\\ 2014\\ The\\ R\\ Foundation\\ for\\ Statistical\\ Computing\n+Platform\\:\\ .*\n+\n+R\\ is\\ free\\ software\\ and\\ comes\\ with\\ ABSOLUTELY\\ NO\\ WARRANTY\\.\n+You\\ are\\ welcome\\ to\\ redistribute\\ it\\ under\\ certain\\ conditions\\.\n+Type\\ \\\'license\\(\\)\\\'\\ or\\ \\\'licence\\(\\)\\\'\\ for\\ distribution\\ details\\.\n+\n+\\ \\ Natural\\ language\\ support\\ but\\ running\\ in\\ an\\ English\\ locale\n+\n+R\\ is\\ a\\ collaborative\\ project\\ with\\ many\\ contributors\\.\n+Type\\ \\\'contributors\\(\\)\\\'\\ for\\ more\\ information\\ and\n+\\\'citation\\(\\)\\\'\\ on\\ how\\ to\\ cite\\ R\\ or\\ R\\ packages\\ in\\ publications\\.\n+\n+Type\\ \\\'demo\\(\\)\\\'\\ for\\ some\\ demos\\,\\ \\\'help\\(\\)\\\'\\ for\\ on\\-line\\ help\\,\\ or\n+\\\'help\\.start\\(\\)\\\'\\ for\\ an\\ HTML\\ browser\\ interface\\ to\\ help\\.\n+Type\\ \\\'q\\(\\)\\\'\\ to\\ quit\\ R\\.\n+\n+\\>\\ \\#\\ ARGUMENTS\\:\\ \n+\\>\\ \\#\\ name\\ \\=\\ ceas\n+\\>\\ \\#\\ gene\\ annotation\\ table\\ \\=\\ .*galGal3\\.refGene\n+\\>\\ \\#\\ BED\\ file\\ \\=\\ .*\n+\\>\\ \\#\\ WIG\\ file\\ \\=\\ .*\n+\\>\\ \\#\\ extra\\ BED\\ file\\ \\=\\ None\n+\\>\\ \\#\\ ChIP\\ annotation\\ \\=\\ On\n+\\>\\ \\#\\ gene\\-centered\\ annotation\\ \\=\\ \\ On\n+\\>\\ \\#\\ average\\ profiling\\ \\=\\ On\n+\\>\\ \\#\\ dump\\ profiles\\ \\=\\ Off\n+\\>\\ \\#\\ re\\-annotation\\ for\\ genome\\ background\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ False\n+\\>\\ \\#\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\>\\ \\#\\ downstream\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 1000\\,2000\\,3000\\ bp\n+\\>\\ \\#\\ bidrectional\\ promoter\\ sizes\\ \\(ChIP\\ region\\ annotation\\)\\ \\=\\ 2500\\,5000\\ bp\n+\\>\\ \\#\\ span\\ size\\ \\(gene\\-centered\\ annotation\\)\\ \\=\\ 3000\\ bp\n+\\>\\ \\#\\ profiling\\ resolution\\ \\(average\\ profiling\\)\\ \\=\\ 50\\ bp\n+\\>\\ \\#\\ relative\\ distance\\ wrt\\ TSS\\ and\\ TTS\\ \\(average\\ profiling\\)\\ \\=\\ 3000\\ bp\n+\\>\\ pdf\\(\\"ceas\\.pdf\\"\\,height\\=11\\.5\\,width\\=8\\.5\\)\n+\\>\\ \n+\\>\\ \\#\\ .*\n+\\>\\ \\#\\ \n+\\>\\ \\#\\ ChIP\\ annotation\n+\\>\\ \\#\\ \n+\\>\\ \n+\\>\\ \n+\\>\\ \\#\\ \n+\\>\\ \\#\\ Chromosomal\\ Distribution\n+\\>\\ \\#\\ \n+\\>\\ \n+\\>\\ par\\(mar\\=c\\(4\\,\\ 4\\,\\ 5\\,\\ 3\\.8\\)\\,oma\\=c\\(4\\,\\ 2\\,\\ 4\\,\\ 2\\)\\)\n+\\>\\ r0\\<\\-c\\(100\\.0\\)\n+\\>\\ r1\\<\\-c\\(100\\.0\\)\n+\\>\\ height\\<\\-rbind\\(r0\\,r1\\)\n+\\>\\ names\\=c\\(\\"26\\"\\)\n+\\>\\ 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\\)\n+\\>\\ text\\(x\\=c\\(100\\.0\\)\\,y\\=mp\\[1\\,\\]\\,label\\=c\\(\\"100\\.0\\ \\%\\'..b'3\\.333333\\,76\\.666667\\,80\\.000000\\,83\\.333333\\,86\\.666667\\,90\\.000000\\,93\\.333333\\,96\\.666667\\,100\\.000000\\)\n+\\>\\ 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\\)\n+\\>\\ 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\\)\n+\\>\\ 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\\)\n+\\>\\ 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\\)\n+\\>\\ 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\\)\n+\\>\\ par\\(mfrow\\=c\\(3\\,\\ 2\\)\\,mar\\=c\\(4\\,\\ 4\\,\\ 5\\,\\ 3\\.8\\)\\,oma\\=c\\(4\\,\\ 2\\,\\ 4\\,\\ 2\\)\\)\n+\\>\\ x\\<\\-c\\(\\-3\\.000000\\,3\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,1\\.000000\\)\n+\\>\\ 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\\"\\)\n+\\>\\ x\\<\\-c\\(\\-3\\.000000\\,3\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,1\\.000000\\)\n+\\>\\ 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\\"\\)\n+\\>\\ x\\<\\-c\\(\\-3\\.000000\\,3\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,1\\.000000\\)\n+\\>\\ 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\\"\\)\n+\\>\\ x\\<\\-c\\(\\-3\\.000000\\,3\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,1\\.000000\\)\n+\\>\\ 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\\"\\)\n+\\>\\ x\\<\\-c\\(\\-3\\.000000\\,3\\.000000\\)\n+\\>\\ y\\<\\-c\\(0\\.000000\\,1\\.000000\\)\n+\\>\\ 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\\"\\)\n+\\>\\ 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\\)\n+\\>\\ 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\\)\n+\\>\\ plot\\(x\\,\\ y\\,type\\=\\"l\\"\\,main\\=\\"Average\\ Intron\\ Profile\n+\\+\\ \\(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\\)\n+\\>\\ dev\\.off\\(\\)\n+null\\ device\\ \n+\\ \\ \\ \\ \\ \\ \\ \\ \\ \\ 1\\ \n+\\>\\ \n+INFO\\ \\ \\@\\ .*\\ \\#\\.\\.\\.\\ cong\\!\\ See\\ ceas\\.pdf\\ for\\ the\\ graphical\\ results\\ of\\ CEAS\\!\\ \n' |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out3.pdf |
| b |
| Binary file test-data/ceas_out3.pdf has changed |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/ceas_out3.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ceas_out3.xls Tue Jun 30 07:08:05 2015 -0400 |
| b |
| b"@@ -0,0 +1,133 @@\n+# RefSeq: RefSeq ID\n+# chr: chromosome of a RefSeq gene\n+# txStart: 5' end of a RefSeq gene\n+# txEnd: 3' end site of a RefSeq gene\n+# strand: strand of a RefSeq gene\n+# dist u TSS: Distance to the nearest ChIP region's center upstream of transcription start site (bp)\n+# dist d TSS: Distance to the nearest ChIP region's center downstream of transcription start site (bp)\n+# dist u TTS: Distance to the nearest ChIP region's center upstream of transcription end site (bp)\n+# dist d TTS: Distance to the nearest ChIP region's center downstream of transcription end (bp)\n+# 3000bp u TSS: Occupancy rate of ChIP region in 3000bp upstream of transcription start site (0.0 - 1.0)\n+# 3000bp d TSS: Occupancy rate of ChIP region in 3000bp downstream of transcription start site (0.0 - 1.0)\n+# 1/3 gene: Occupancy rate of ChIP region in 1/3 gene (0.0 - 1.0)\n+# 2/3 gene: Occupancy rate of ChIP region in 2/3 gene (0.0 - 1.0)\n+# 3/3 gene: Occupancy rate of ChIP region in 3/3 gene (0.0 - 1.0)\n+# 3000bp d TTS: Occupancy rate of ChIP region in 3000bp downstream of transcriptino end (0.0 - 1.0)\n+# exons: Occupancy rate of ChIP regions in exons (0.0-1.0)\n+# 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.\n+#name\tchr\ttxStart\ttxEnd\tstrand\tdist u TSS\tdist d TSS\tdist u TTS\tdist d TTS\t3000bp u TSS\t3000bp d TSS\t1/3 gene\t2/3 gene\t3/3 gene\t3000bp d TTS\texons\n+NM_001031576\tchr26\t19281\t27136\t+\tNA\t4099848\tNA\t4091993\t0\t0\t0\t0\t0\t0\t0\n+NM_204615\tchr26\t57466\t61594\t-\t4057535\tNA\t4061663\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001005431\tchr26\t65800\t76175\t-\t4042954\tNA\t4053329\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001145491\tchr26\t91618\t92166\t-\t4026963\tNA\t4027511\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204398\tchr26\t93069\t97423\t+\tNA\t4026060\tNA\t4021706\t0\t0\t0\t0\t0\t0\t0\n+NM_001305147\tchr26\t254661\t282571\t+\tNA\t3864468\tNA\t3836558\t0\t0\t0\t0\t0\t0\t0\n+NM_001305148\tchr26\t254661\t282571\t+\tNA\t3864468\tNA\t3836558\t0\t0\t0\t0\t0\t0\t0\n+NM_001012868\tchr26\t350397\t355252\t-\t3763877\tNA\t3768732\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001031030\tchr26\t479573\t493561\t+\tNA\t3639556\tNA\t3625568\t0\t0\t0\t0\t0\t0\t0\n+NM_001305140\tchr26\t520705\t526012\t+\tNA\t3598424\tNA\t3593117\t0\t0\t0\t0\t0\t0\t0\n+NM_001031029\tchr26\t537101\t565572\t+\tNA\t3582028\tNA\t3553557\t0\t0\t0\t0\t0\t0\t0\n+NM_205248\tchr26\t537250\t760479\t+\tNA\t3581879\tNA\t3358650\t0\t0\t0\t0\t0\t0\t0\n+NM_204727\tchr26\t662969\t683066\t-\t3436063\tNA\t3456160\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_105475\tchr26\t669012\t669122\t-\t3450007\tNA\t3450117\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205449\tchr26\t785617\t794076\t+\tNA\t3333512\tNA\t3325053\t0\t0\t0\t0\t0\t0\t0\n+NM_204681\tchr26\t897458\t902049\t-\t3217080\tNA\t3221671\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001278156\tchr26\t905313\t917094\t-\t3202035\tNA\t3213816\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204184\tchr26\t960209\t964268\t-\t3154861\tNA\t3158920\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204316\tchr26\t974223\t991244\t+\tNA\t3144906\tNA\t3127885\t0\t0\t0\t0\t0\t0\t0\n+NM_001031028\tchr26\t993815\t1003847\t-\t3115282\tNA\t3125314\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006392\tchr26\t1024606\t1047756\t-\t3071373\tNA\t3094523\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001039596\tchr26\t1073550\t1080033\t-\t3039096\tNA\t3045579\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001031027\tchr26\t1090460\t1096137\t+\tNA\t3028669\tNA\t3022992\t0\t0\t0\t0\t0\t0\t0\n+NM_001031026\tchr26\t1096566\t1104751\t-\t3014378\tNA\t3022563\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030913\tchr26\t1122296\t1132596\t+\tNA\t2996833\tNA\t2986533\t0\t0\t0\t0\t0\t0\t0\n+NM_001171886\tchr26\t1220031\t1222791\t-\t2896338\tNA\t2899098\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205054\tchr26\t1229703\t1232833\t+\tNA\t2889426\tNA\t2886296\t0\t0\t0\t0\t0\t0\t0\n+NM_204462\tchr26\t1234686\t1236536\t-\t2882593\tNA\t2884443\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204463\tchr26\t1265724\t1267989\t-\t2851140\tNA\t2853405\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030378\tchr26\t1289091\t1290386\t-\t2828743\tNA\t2830038\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001195554\tchr26\t1382510\t1388447\t+\tNA\t2736619\tNA\t2730682\t0\t0\t0\t0\t0\t0\t0\n+NM_001012548\tchr26\t1406905\t1428443\t+\tNA\t2712224\tNA\t2690686\t0\t0\t0\t0\t0\t0\t0\n+NR_031486\tchr26\t1442696\t1442779\t-\t2676350\tNA\t2676433\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_031487\tchr26\t1442896\t1442979\t-\t2676150\tNA\t2676233\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205250\tchr26\t1472137\t1474003\t+\tNA\t2646992\tNA\t2645126\t0\t0\t0\t0\t0\t0\t0\n+NR_105486\tchr26\t1566398\t1566508\t-\t2552621\tNA"..b'4101\t0\t0\t0\t0\t0\t0\t0\n+NM_204664\tchr26\t2498398\t2509349\t+\tNA\t1620731\tNA\t1609780\t0\t0\t0\t0\t0\t0\t0\n+NR_031489\tchr26\t2511657\t2511746\t-\t1607383\tNA\t1607472\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_031490\tchr26\t2512568\t2512648\t-\t1606481\tNA\t1606561\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_105523\tchr26\t2669792\t2669902\t-\t1449227\tNA\t1449337\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_031491\tchr26\t2896046\t2896142\t+\tNA\t1223083\tNA\t1222987\t0\t0\t0\t0\t0\t0\t0\n+NM_001190924\tchr26\t2961382\t2962268\t+\tNA\t1157747\tNA\t1156861\t0\t0\t0\t0\t0\t0\t0\n+NM_001007881\tchr26\t2999189\t3002725\t+\tNA\t1119940\tNA\t1116404\t0\t0\t0\t0\t0\t0\t0\n+NM_204320\tchr26\t3006741\t3011817\t-\t1107312\tNA\t1112388\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030916\tchr26\t3035271\t3039335\t-\t1079794\tNA\t1083858\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204151\tchr26\t3047964\t3050306\t-\t1068823\tNA\t1071165\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204326\tchr26\t3124816\t3214381\t-\t904748\tNA\t994313\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204336\tchr26\t3320769\t3332327\t+\tNA\t798360\tNA\t786802\t0\t0\t0\t0\t0\t0\t0\n+NM_204622\tchr26\t3339753\t3358863\t-\t760266\tNA\t779376\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205515\tchr26\t3359016\t3368964\t+\tNA\t760113\tNA\t750165\t0\t0\t0\t0\t0\t0\t0\n+NM_001012843\tchr26\t3370712\t3377196\t+\tNA\t748417\tNA\t741933\t0\t0\t0\t0\t0\t0\t0\n+NM_001029849\tchr26\t3377655\t3382628\t-\t736501\tNA\t741474\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006323\tchr26\t3439841\t3454783\t-\t664346\tNA\t679288\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_035162\tchr26\t3455233\t3455324\t+\tNA\t663896\tNA\t663805\t0\t0\t0\t0\t0\t0\t0\n+NM_001012697\tchr26\t3516478\t3545774\t+\tNA\t602651\tNA\t573355\t0\t0\t0\t0\t0\t0\t0\n+NM_001030917\tchr26\t3590932\t3597509\t-\t521620\tNA\t528197\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001031500\tchr26\t3597231\t3600802\t+\tNA\t521898\tNA\t518327\t0\t0\t0\t0\t0\t0\t0\n+NM_001040018\tchr26\t3629575\t3631171\t+\tNA\t489554\tNA\t487958\t0\t0\t0\t0\t0\t0\t0\n+NM_001257295\tchr26\t3698350\t3701362\t-\t417767\tNA\t420779\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001257296\tchr26\t3701377\t3715857\t-\t403272\tNA\t417752\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001012549\tchr26\t3735643\t3742472\t-\t376657\tNA\t383486\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030918\tchr26\t3742618\t3760175\t-\t358954\tNA\t376511\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006324\tchr26\t3760758\t3765368\t-\t353761\tNA\t358371\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205063\tchr26\t3809805\t3812700\t+\tNA\t309324\tNA\t306429\t0\t0\t0\t0\t0\t0\t0\n+NM_001293109\tchr26\t3859074\t3879130\t-\t239999\tNA\t260055\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001293108\tchr26\t3859074\t3882051\t-\t237078\tNA\t260055\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_102328\tchr26\t3916006\t3918143\t-\t200986\tNA\t203123\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204728\tchr26\t3920817\t3937442\t-\t181687\tNA\t198312\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001244905\tchr26\t4104910\t4108376\t+\tNA\t14219\tNA\t10753\t0\t0\t0\t0\t0\t0\t0\n+NM_001293166\tchr26\t4138324\t4142325\t-\tNA\t23196\tNA\t19195\t0\t0\t0\t0\t0\t0\t0\n+NM_001030919\tchr26\t4144091\t4175943\t+\t24962\tNA\t56814\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001257297\tchr26\t4209891\t4216177\t+\t90762\tNA\t97048\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001257298\tchr26\t4218028\t4238067\t+\t98899\tNA\t118938\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_205490\tchr26\t4375371\t4380959\t-\tNA\t261830\tNA\t256242\t0\t0\t0\t0\t0\t0\t0\n+NM_001305129\tchr26\t4391940\t4397490\t+\t272811\tNA\t278361\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001271612\tchr26\t4433568\t4438784\t+\t314439\tNA\t319655\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030920\tchr26\t4498991\t4730550\t+\t379862\tNA\t611421\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001030921\tchr26\t4541748\t4544997\t-\tNA\t425868\tNA\t422619\t0\t0\t0\t0\t0\t0\t0\n+NM_001006325\tchr26\t4548211\t4559974\t+\t429082\tNA\t440845\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001037832\tchr26\t4571684\t4576072\t-\tNA\t456943\tNA\t452555\t0\t0\t0\t0\t0\t0\t0\n+NM_001080870\tchr26\t4578266\t4580646\t-\tNA\t461517\tNA\t459137\t0\t0\t0\t0\t0\t0\t0\n+NM_001080868\tchr26\t4578266\t4580647\t-\tNA\t461518\tNA\t459137\t0\t0\t0\t0\t0\t0\t0\n+NM_001030922\tchr26\t4730394\t4744364\t-\tNA\t625235\tNA\t611265\t0\t0\t0\t0\t0\t0\t0\n+NM_204877\tchr26\t4751619\t4755464\t-\tNA\t636335\tNA\t632490\t0\t0\t0\t0\t0\t0\t0\n+NM_001302134\tchr26\t4791084\t4792014\t+\t671955\tNA\t672885\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_001006327\tchr26\t4828534\t4833077\t-\tNA\t713948\tNA\t709405\t0\t0\t0\t0\t0\t0\t0\n+NM_001008453\tchr26\t4838545\t4850970\t-\tNA\t731841\tNA\t719416\t0\t0\t0\t0\t0\t0\t0\n+NM_001030923\tchr26\t4876559\t4884910\t+\t757430\tNA\t765781\tNA\t0\t0\t0\t0\t0\t0\t0\n+NM_204429\tchr26\t4897094\t4901738\t-\tNA\t782609\tNA\t777965\t0\t0\t0\t0\t0\t0\t0\n+NM_204967\tchr26\t4946735\t4952662\t-\tNA\t833533\tNA\t827606\t0\t0\t0\t0\t0\t0\t0\n+NM_204473\tchr26\t4990765\t4993729\t+\t871636\tNA\t874600\tNA\t0\t0\t0\t0\t0\t0\t0\n+NR_105623\tchr26\t5087926\t5087980\t-\tNA\t968851\tNA\t968797\t0\t0\t0\t0\t0\t0\t0\n' |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/galGal3.len --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/galGal3.len Tue Jun 30 07:08:05 2015 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r f411ce97a351 test-data/galGal3.refGene |
| b |
| Binary file test-data/galGal3.refGene has changed |
| b |
| diff -r 000000000000 -r f411ce97a351 tool-data/ceas.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ceas.loc.sample Tue Jun 30 07:08:05 2015 -0400 |
| b |
| @@ -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. |
| b |
| diff -r 000000000000 -r f411ce97a351 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 30 07:08:05 2015 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r f411ce97a351 tool_data_table_conf.xml.test --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r f411ce97a351 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jun 30 07:08:05 2015 -0400 |
| b |
| @@ -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 && + 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 && + 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> |