Mercurial > repos > devteam > sicer
changeset 0:82a8234e03f2 draft
Imported from capsule None
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sicer_wrapper.py Mon Jan 27 09:28:33 2014 -0500 @@ -0,0 +1,157 @@ +#!/usr/bin/env python +#Dan Blankenberg + +""" +A wrapper script for running SICER (spatial clustering approach for the identification of ChIP-enriched regions) region caller. +""" + +import sys, optparse, os, tempfile, subprocess, shutil + +CHUNK_SIZE = 2**20 #1mb + +#HACK! FIXME: allow using all specified builds, would currently require hacking SICER's "GenomeData.py" on the fly. +VALID_BUILDS = [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ] + +def cleanup_before_exit( tmp_dir ): + if tmp_dir and os.path.exists( tmp_dir ): + shutil.rmtree( tmp_dir ) + + +def open_file_from_option( filename, mode = 'rb' ): + if filename: + return open( filename, mode = mode ) + return None + +def add_one_to_file_column( filename, column, split_char = "\t", startswith_skip = None ): + tmp_out = tempfile.TemporaryFile( mode='w+b' ) + tmp_in = open( filename ) + for line in tmp_in: + if startswith_skip and line.startswith( startswith_skip ): + tmp_out.write( line ) + else: + fields = line.rstrip( '\n\r' ).split( split_char ) + if len( fields ) <= column: + tmp_out.write( line ) + else: + fields[ column ] = str( int( fields[ column ] ) + 1 ) + tmp_out.write( "%s\n" % ( split_char.join( fields ) ) ) + tmp_in.close() + tmp_out.seek( 0 ) + tmp_in = open( filename, 'wb' ) + while True: + chunk = tmp_out.read( CHUNK_SIZE ) + if chunk: + tmp_in.write( chunk ) + else: + break + tmp_in.close() + tmp_out.close() + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + #stdout/err + parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' ) + parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' ) + parser.add_option( '', '--fix_off_by_one_errors', dest='fix_off_by_one_errors', action='store_true', default=False, help='If specified, fix off-by-one errors in output files' ) + #inputs + parser.add_option( '-b', '--bed_file', dest='bed_file', action='store', type="string", default=None, help='Input ChIP BED file.' ) + parser.add_option( '-c', '--control_file', dest='control_file', action='store', type="string", default=None, help='Input control BED file.' ) + parser.add_option( '-d', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='Input dbkey.' ) + parser.add_option( '-r', '--redundancy_threshold', dest='redundancy_threshold', action='store', type="int", default=1, help='Redundancy Threshold: The number of copies of identical reads allowed in a library.' ) + parser.add_option( '-w', '--window_size', dest='window_size', action='store', type="int", default=200, help='Window size: resolution of SICER algorithm. For histone modifications, one can use 200 bp' ) + parser.add_option( '-f', '--fragment_size', dest='fragment_size', action='store', type="int", default=150, help='Fragment size: is for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75.' ) + parser.add_option( '-e', '--effective_genome_fraction', dest='effective_genome_fraction', action='store', type="float", default=0.74, help='Effective genome fraction: Effective Genome as fraction of the genome size. It depends on read length.' ) + parser.add_option( '-g', '--gap_size', dest='gap_size', action='store', type="int", default=600, help='Gap size: needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ... .' ) + parser.add_option( '-o', '--error_cut_off', dest='error_cut_off', action='store', type="string", default="0.1", help='Error Cut off: FDR or E-value' ) #read as string to construct names properly + #outputs + parser.add_option( '', '--redundancy_removed_test_bed_output_file', dest='redundancy_removed_test_bed_output_file', action='store', type="string", default=None, help='test-1-removed.bed: redundancy_removed test bed file' ) + parser.add_option( '', '--redundancy_removed_control_bed_output_file', dest='redundancy_removed_control_bed_output_file', action='store', type="string", default=None, help='control-1-removed.bed: redundancy_removed control bed file' ) + parser.add_option( '', '--summary_graph_output_file', dest='summary_graph_output_file', action='store', type="string", default=None, help='test-W200.graph: summary graph file for test-1-removed.bed with window size 200, in bedGraph format.' ) + parser.add_option( '', '--test_normalized_wig_output_file', dest='test_normalized_wig_output_file', action='store', type="string", default=None, help='test-W200-normalized.wig: the above file normalized by library size per million and converted into wig format. This file can be uploaded to the UCSC genome browser' ) + parser.add_option( '', '--score_island_output_file', dest='score_island_output_file', action='store', type="string", default=None, help='test-W200-G600.scoreisland: an intermediate file for debugging usage.' ) + parser.add_option( '', '--islands_summary_output_file', dest='islands_summary_output_file', action='store', type="string", default=None, help='test-W200-G600-islands-summary: summary of all candidate islands with their statistical significance.' ) + parser.add_option( '', '--significant_islands_summary_output_file', dest='significant_islands_summary_output_file', action='store', type="string", default=None, help='test-W200-G600-islands-summary-FDR.01: summary file of significant islands with requirement of FDR=0.01.' ) + parser.add_option( '', '--significant_islands_output_file', dest='significant_islands_output_file', action='store', type="string", default=None, help='test-W200-G600-FDR.01-island.bed: delineation of significant islands in "chrom start end read-count-from-redundancy_removed-test.bed" format' ) + parser.add_option( '', '--island_filtered_output_file', dest='island_filtered_output_file', action='store', type="string", default=None, help='test-W200-G600-FDR.01-islandfiltered.bed: library of raw redundancy_removed reads on significant islands.' ) + parser.add_option( '', '--island_filtered_normalized_wig_output_file', dest='island_filtered_normalized_wig_output_file', action='store', type="string", default=None, help='test-W200-G600-FDR.01-islandfiltered-normalized.wig: wig file for the island-filtered redundancy_removed reads.' ) + (options, args) = parser.parse_args() + + #check if valid build + assert options.dbkey in VALID_BUILDS, ValueError( "The specified build ('%s') is not available for this tool." % options.dbkey ) + + #everything will occur in this temp directory + tmp_dir = tempfile.mkdtemp() + + #link input files into tmp_dir and build command line + bed_base_filename = 'input_bed_file' + bed_filename = '%s.bed' % bed_base_filename + os.symlink( options.bed_file, os.path.join( tmp_dir, bed_filename ) ) + if options.control_file is not None: + cmd = "SICER.sh" + else: + cmd = "SICER-rb.sh" + cmd = '%s "%s" "%s"' % ( cmd, tmp_dir, bed_filename ) + if options.control_file is not None: + control_base_filename = 'input_control_file' + control_filename = '%s.bed' % control_base_filename + os.symlink( options.control_file, os.path.join( tmp_dir, control_filename ) ) + cmd = '%s "%s"' % ( cmd, control_filename ) + cmd = '%s "%s" "%s" "%i" "%i" "%i" "%f" "%i" "%s"' % ( cmd, tmp_dir, options.dbkey, options.redundancy_threshold, options.window_size, options.fragment_size, options.effective_genome_fraction, options.gap_size, options.error_cut_off ) + + #set up stdout and stderr output options + stdout = open_file_from_option( options.stdout, mode = 'wb' ) + stderr = open_file_from_option( options.stderr, mode = 'wb' ) + #if no stderr file is specified, we'll use our own + if stderr is None: + stderr = tempfile.NamedTemporaryFile( dir=tmp_dir ) + stderr.close() + stderr = open( stderr.name, 'w+b' ) + + proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) + return_code = proc.wait() + + if return_code: + stderr_target = sys.stderr + else: + stderr_target = stdout #sys.stdout + stderr_target.write( "\nAdditionally, these warnings were reported:\n" ) + stderr.flush() + stderr.seek(0) + while True: + chunk = stderr.read( CHUNK_SIZE ) + if chunk: + stderr_target.write( chunk ) + else: + break + stderr.close() + + try: + #move files to where they belong + shutil.move( os.path.join( tmp_dir,'%s-%i-removed.bed' % ( bed_base_filename, options.redundancy_threshold ) ), options.redundancy_removed_test_bed_output_file ) + shutil.move( os.path.join( tmp_dir,'%s-W%i.graph' % ( bed_base_filename, options.window_size ) ), options.summary_graph_output_file ) + if options.fix_off_by_one_errors: add_one_to_file_column( options.summary_graph_output_file, 2 ) + shutil.move( os.path.join( tmp_dir,'%s-W%i-normalized.wig' % ( bed_base_filename, options.window_size ) ), options.test_normalized_wig_output_file ) + if options.control_file is not None: + shutil.move( os.path.join( tmp_dir,'%s-%i-removed.bed' % ( control_base_filename, options.redundancy_threshold ) ), options.redundancy_removed_control_bed_output_file ) + shutil.move( os.path.join( tmp_dir,'%s-W%i-G%i.scoreisland' % ( bed_base_filename, options.window_size, options.gap_size ) ), options.score_island_output_file ) + if options.fix_off_by_one_errors: add_one_to_file_column( options.score_island_output_file, 2 ) + shutil.move( os.path.join( tmp_dir,'%s-W%i-G%i-islands-summary' % ( bed_base_filename, options.window_size, options.gap_size ) ), options.islands_summary_output_file ) + if options.fix_off_by_one_errors: add_one_to_file_column( options.islands_summary_output_file, 2 ) + shutil.move( os.path.join( tmp_dir,'%s-W%i-G%i-islands-summary-FDR%s' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.significant_islands_summary_output_file ) + if options.fix_off_by_one_errors: add_one_to_file_column( options.significant_islands_summary_output_file, 2 ) + shutil.move( os.path.join( tmp_dir,'%s-W%i-G%i-FDR%s-island.bed' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.significant_islands_output_file ) + if options.fix_off_by_one_errors: add_one_to_file_column( options.significant_islands_output_file, 2 ) + shutil.move( os.path.join( tmp_dir,'%s-W%i-G%i-FDR%s-islandfiltered.bed' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_output_file ) + shutil.move( os.path.join( tmp_dir,'%s-W%i-G%i-FDR%s-islandfiltered-normalized.wig' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_normalized_wig_output_file ) + else: + shutil.move( os.path.join( tmp_dir,'%s-W%i-G%i-E%s.scoreisland' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.score_island_output_file ) + if options.fix_off_by_one_errors: add_one_to_file_column( options.score_island_output_file, 2 ) + shutil.move( os.path.join( tmp_dir,'%s-W%i-G%i-E%s-islandfiltered.bed' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_output_file ) + shutil.move( os.path.join( tmp_dir,'%s-W%i-G%i-E%s-islandfiltered-normalized.wig' % ( bed_base_filename, options.window_size, options.gap_size, options.error_cut_off ) ), options.island_filtered_normalized_wig_output_file ) + except Exception, e: + raise e + finally: + cleanup_before_exit( tmp_dir ) + +if __name__=="__main__": __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sicer_wrapper.xml Mon Jan 27 09:28:33 2014 -0500 @@ -0,0 +1,178 @@ +<tool id="peakcalling_sicer" name="SICER" version="0.0.1"> + <description>Statistical approach for the Identification of ChIP-Enriched Regions</description> + <command interpreter="python">sicer_wrapper.py + --bed_file '${input_bed_file}' + #if str( $input_control_file ) != 'None': + --control_file '${input_control_file}' + --significant_islands_output_file "${significant_islands_output_file}" + --islands_summary_output_file "${islands_summary_output_file}" + --significant_islands_summary_output_file "${significant_islands_summary_output_file}" + #end if + ${fix_off_by_one_errors} + --dbkey '${input_bed_file.dbkey}' + --redundancy_threshold '${redundancy_threshold}' + --window_size '${window_size}' + --fragment_size '${fragment_size}' + --effective_genome_fraction '${effective_genome_fraction}' + --gap_size '${gap_size}' + --error_cut_off '${error_cut_off}' + ##output files + --stdout "${output_log_file}" + --redundancy_removed_test_bed_output_file "${redundancy_removed_test_bed_output_file}" + --redundancy_removed_control_bed_output_file "${redundancy_removed_control_bed_output_file}" + --score_island_output_file "${score_island_output_file}" + --summary_graph_output_file "${summary_graph_output_file}" + --test_normalized_wig_output_file "${test_normalized_wig_output_file}" + --island_filtered_output_file "${island_filtered_output_file}" + --island_filtered_normalized_wig_output_file "${island_filtered_normalized_wig_output_file}" + </command> + <requirements> + <requirement type="package" version="1.1">SICER</requirement> + </requirements> + <inputs> + <param name="input_bed_file" type="data" format="bed" label="ChIP-Seq Tag File" > + <validator type="expression" message="SICER is not available for the genome.">value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]</validator> + </param> + <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" optional="True"> <!-- fix me, add filter to match dbkeys --> + <options> + <filter type="data_meta" ref="input_bed_file" key="dbkey" /> + </options> + </param> + <param name="fix_off_by_one_errors" type="boolean" truevalue="--fix_off_by_one_errors" falsevalue="" checked="True" label="Fix off-by-one errors in output files" help="SICER creates non-standard output files, this option will fix these coordinates"/> + <param name="redundancy_threshold" type="integer" label="Redundancy Threshold" value="1" help="The number of copies of identical reads allowed in a library" /> + <param name="window_size" type="integer" label="Window size" value="200" help="Resolution of SICER algorithm. For histone modifications, one can use 200 bp" /> + <param name="fragment_size" type="integer" label="Fragment size" value="150" help="for determination of the amount of shift from the beginning of a read to the center of the DNA fragment represented by the read. FRAGMENT_SIZE=150 means the shift is 75." /> + <param name="effective_genome_fraction" type="float" label="Effective genome fraction" value="0.74" help="Effective Genome as fraction of the genome size. It depends on read length." /> + <param name="gap_size" type="integer" label="Gap size" value="600" help="Needs to be multiples of window size. Namely if the window size is 200, the gap size should be 0, 200, 400, 600, ..." /> + <param name="error_cut_off" type="float" label="Statistic threshold value" value="0.01" help="FDR (with control) or E-value (without control)" /> + </inputs> + <outputs> + <data name="redundancy_removed_test_bed_output_file" format="bed" label="${tool.name} on ${on_string} (test-${redundancy_threshold}-removed.bed)"/> + <data name="redundancy_removed_control_bed_output_file" format="bed" label="${tool.name} on ${on_string} (control-${redundancy_threshold}-removed.bed)"> + <filter>input_control_file is not None</filter> + </data> + <data name="summary_graph_output_file" format="bedgraph" label="${tool.name} on ${on_string} (test-W${window_size}.graph)"/> + <data name="test_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (test-W${window_size}-normalized.wig)"/> + <data name="significant_islands_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-FDR${error_cut_off}-island.bed)"> + <filter>input_control_file is not None</filter> + </data> + <data name="island_filtered_output_file" format="bed" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered.bed' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered.bed' ] ) ) #)"/> + <data name="island_filtered_normalized_wig_output_file" format="wig" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '-FDR', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '-islandfiltered-normalized.wig' ] ) ) #)"/> + <data name="score_island_output_file" format="interval" label="${tool.name} on ${on_string} (#if str( $input_control_file ) != 'None' then ''.join( map( str, [ 'test-W', $window_size, '-G',$gap_size, '.scoreisland' ] ) ) else ''.join( map( str, [ 'test-W', $window_size, '-G', $gap_size, '-E', $error_cut_off, '.scoreisland' ] ) ) #)"/> + <data name="islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary)"> + <filter>input_control_file is not None</filter> + </data> + <data name="significant_islands_summary_output_file" format="interval" label="${tool.name} on ${on_string} (test-W${window_size}-G${gap_size}-islands-summary-FDR${error_cut_off})"> + <filter>input_control_file is not None</filter> + </data> + <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> + </outputs> + <tests> + <test> + <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> + <param name="input_control_file" /> + <param name="fix_off_by_one_errors" /> + <param name="redundancy_threshold" value="1" /> + <param name="window_size" value="200" /> + <param name="fragment_size" value="150" /> + <param name="effective_genome_fraction" value="0.74" /> + <param name="gap_size" value="600" /> + <param name="error_cut_off" value="0.01" /> + <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" /> + <output name="summary_graph_output_file" file="peakcalling_sicer/test_1/test-W200.graph" /> + <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" /> + <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" /> + <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" /> + <output name="score_island_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01.scoreisland" /> + <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/> + </test> + <test> + <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> + <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" /> + <param name="fix_off_by_one_errors" /> + <param name="redundancy_threshold" value="1" /> + <param name="window_size" value="200" /> + <param name="fragment_size" value="150" /> + <param name="effective_genome_fraction" value="0.74" /> + <param name="gap_size" value="600" /> + <param name="error_cut_off" value="0.01" /> + <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" /> + <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" /> + <output name="summary_graph_output_file" file="peakcalling_sicer/test_2/test-W200.graph" /> + <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" /> + <output name="significant_islands_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed" /> + <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" /> + <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" /> + <output name="score_island_output_file" file="peakcalling_sicer/test_2/test-W200-G600.scoreisland" /> + <output name="islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary" /> + <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01" /> + <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/> + </test> + <test> + <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> + <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="mm8" /> + <param name="fix_off_by_one_errors" value="True" /> + <param name="redundancy_threshold" value="1" /> + <param name="window_size" value="200" /> + <param name="fragment_size" value="150" /> + <param name="effective_genome_fraction" value="0.74" /> + <param name="gap_size" value="600" /> + <param name="error_cut_off" value="0.01" /> + <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_2/test-1-removed.bed" /> + <output name="redundancy_removed_control_bed_output_file" file="peakcalling_sicer/test_2/control-1-removed.bed" /> + <output name="summary_graph_output_file" file="peakcalling_sicer/test_3/test-W200.graph" /> + <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-normalized.wig" /> + <output name="significant_islands_output_file" file="peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed" /> + <output name="island_filtered_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed" /> + <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig" /> + <output name="score_island_output_file" file="peakcalling_sicer/test_3/test-W200-G600.scoreisland" /> + <output name="islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary" /> + <output name="significant_islands_summary_output_file" file="peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01" /> + <output name="output_log_file" file="peakcalling_sicer/test_2/output_log_file.contains" compare="contains"/> + </test> + <test> + <param name="input_bed_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="mm8" /> + <param name="input_control_file" /> + <param name="fix_off_by_one_errors" value="True" /> + <param name="redundancy_threshold" value="1" /> + <param name="window_size" value="200" /> + <param name="fragment_size" value="150" /> + <param name="effective_genome_fraction" value="0.74" /> + <param name="gap_size" value="600" /> + <param name="error_cut_off" value="0.01" /> + <output name="redundancy_removed_test_bed_output_file" file="peakcalling_sicer/test_1/test-1-removed.bed" /> + <output name="summary_graph_output_file" file="peakcalling_sicer/test_4/test-W200.graph" /> + <output name="test_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-normalized.wig" /> + <output name="island_filtered_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed" /> + <output name="island_filtered_normalized_wig_output_file" file="peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig" /> + <output name="score_island_output_file" file="peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland" /> + <output name="output_log_file" file="peakcalling_sicer/test_1/output_log_file.contains" compare="contains"/> + </test> + </tests> + <help> +**What it does** + +SICER first and foremost is a filtering tool. Its main functions are:: + + 1. Delineation of the significantly ChIP-enriched regions, which can be used to associate with other genomic landmarks. + 2. Identification of reads on the ChIP-enriched regions, which can be used for profiling and other quantitative analysis. + +View the original SICER documentation: http://home.gwu.edu/~wpeng/Software.htm. + +------ + +.. class:: warningmark + + By default, SICER creates files that do not conform to standards (e.g. BED files are closed, not half-open). This could have implications for downstream analysis. + To force the output of SICER to be formatted properly to standard file formats, check the **"Fix off-by-one errors in output files"** option. + +------ + +**Citation** + +For the underlying tool, please cite `Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics. 2009 Aug 1;25(15):1952-8. <http://www.ncbi.nlm.nih.gov/pubmed/19505939>`_ + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_1/output_log_file.contains Mon Jan 27 09:28:33 2014 -0500 @@ -0,0 +1,190 @@ +############################################# +###### SICER v1.1 ###### +############################################# +Input library directory: +ChIP library: +Output directory: +Species: mm8 +Threshold for redundancy allowed for reads: 1 +Window size: 200 bps +Fragment size: 150 bps. The shift for reads is half of 150 +Effective genome size as a fraction of the reference genome of mm8: 0.740000 +Gap size: 600 bps +Evalue for identification of significant islands: 0.01 +Preprocess the raw input_bed_file file to remove redundancy with threshold 1... +chr1 Plus reads: 4989 Retained plus reads: 4935 ; Minus reads: 5011 Retained minus reads: 4963 +chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +Partion the genome in windows ... +Generate summary files for input_bed_file... +total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0 +total tag count in chr2.bed is: 0.0 = 0.0+0.0 +total tag count in chr3.bed is: 0.0 = 0.0+0.0 +total tag count in chr4.bed is: 0.0 = 0.0+0.0 +total tag count in chr5.bed is: 0.0 = 0.0+0.0 +total tag count in chr6.bed is: 0.0 = 0.0+0.0 +total tag count in chr7.bed is: 0.0 = 0.0+0.0 +total tag count in chr8.bed is: 0.0 = 0.0+0.0 +total tag count in chr9.bed is: 0.0 = 0.0+0.0 +total tag count in chr10.bed is: 0.0 = 0.0+0.0 +total tag count in chr11.bed is: 0.0 = 0.0+0.0 +total tag count in chr12.bed is: 0.0 = 0.0+0.0 +total tag count in chr13.bed is: 0.0 = 0.0+0.0 +total tag count in chr14.bed is: 0.0 = 0.0+0.0 +total tag count in chr15.bed is: 0.0 = 0.0+0.0 +total tag count in chr16.bed is: 0.0 = 0.0+0.0 +total tag count in chr17.bed is: 0.0 = 0.0+0.0 +total tag count in chr18.bed is: 0.0 = 0.0+0.0 +total tag count in chr19.bed is: 0.0 = 0.0+0.0 +total tag count in chrX.bed is: 0.0 = 0.0+0.0 +total tag count in chrY.bed is: 0.0 = 0.0+0.0 +total tag count in chrM.bed is: 0.0 = 0.0+0.0 +Normalize summary graph by total redundancy-removed reads per million for input_bed_file ... +Convert the normalized summary graph into wig vstep format... +Find significant islands with E-value 0.01 for input_bed_file... +Species: mm8 +Window_size: 200 +Gap size: 600 +E value is: 0.01 +Total read count: 9898.0 +Genome Length: 2644093988 +Effective genome Length: 1956629551 +Window average: 0.0010117398048 +Window pvalue: 0.2 +Minimum num of tags in a qualified window: 1 +Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows +Determine the score threshold from random background +The score threshold is: 21.384 +Make and write islands +Total number of islands: 352 +Filter reads with identified significant islands for input_bed_file... +Make summary graph with filtered reads for input_bed_file... +total tag count in chr1.bed is: 9654.0 = 4808.0+4846.0 +total tag count in chr2.bed is: 0.0 = 0.0+0.0 +total tag count in chr3.bed is: 0.0 = 0.0+0.0 +total tag count in chr4.bed is: 0.0 = 0.0+0.0 +total tag count in chr5.bed is: 0.0 = 0.0+0.0 +total tag count in chr6.bed is: 0.0 = 0.0+0.0 +total tag count in chr7.bed is: 0.0 = 0.0+0.0 +total tag count in chr8.bed is: 0.0 = 0.0+0.0 +total tag count in chr9.bed is: 0.0 = 0.0+0.0 +total tag count in chr10.bed is: 0.0 = 0.0+0.0 +total tag count in chr11.bed is: 0.0 = 0.0+0.0 +total tag count in chr12.bed is: 0.0 = 0.0+0.0 +total tag count in chr13.bed is: 0.0 = 0.0+0.0 +total tag count in chr14.bed is: 0.0 = 0.0+0.0 +total tag count in chr15.bed is: 0.0 = 0.0+0.0 +total tag count in chr16.bed is: 0.0 = 0.0+0.0 +total tag count in chr17.bed is: 0.0 = 0.0+0.0 +total tag count in chr18.bed is: 0.0 = 0.0+0.0 +total tag count in chr19.bed is: 0.0 = 0.0+0.0 +total tag count in chrX.bed is: 0.0 = 0.0+0.0 +total tag count in chrY.bed is: 0.0 = 0.0+0.0 +total tag count in chrM.bed is: 0.0 = 0.0+0.0 +Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million... +Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million... +Done! +Additionally, these warnings were reported: +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_1/test-1-removed.bed Mon Jan 27 09:28:33 2014 -0500 @@ -0,0 +1,9898 @@ +chr1 3002286 3002322 region_1 0 + +chr1 3002729 3002765 region_3 0 + +chr1 3002805 3002841 region_4 0 + +chr1 3003028 3003064 region_6 0 + +chr1 3003396 3003432 region_8 0 + +chr1 3003492 3003528 region_9 0 + +chr1 3004029 3004065 region_10 0 + +chr1 3004174 3004210 region_11 0 + +chr1 3004969 3005005 region_12 0 + +chr1 3005783 3005819 region_13 0 + +chr1 3017794 3017830 region_15 0 + +chr1 3018455 3018491 region_16 0 + +chr1 3018653 3018689 region_18 0 + +chr1 3018889 3018925 region_19 0 + +chr1 3019304 3019340 region_21 0 + +chr1 3019346 3019382 region_22 0 + +chr1 3019560 3019596 region_23 0 + +chr1 3019905 3019941 region_25 0 + +chr1 3020128 3020164 region_26 0 + +chr1 3020299 3020335 region_27 0 + +chr1 3020303 3020339 region_28 0 + +chr1 3020996 3021032 region_29 0 + +chr1 3021378 3021414 region_33 0 + +chr1 3022271 3022307 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4639280 region_9849 0 - +chr1 4641241 4641277 region_9852 0 - +chr1 4641335 4641371 region_9853 0 - +chr1 4641663 4641699 region_9855 0 - +chr1 4641708 4641744 region_9857 0 - +chr1 4641729 4641765 region_9858 0 - +chr1 4641824 4641860 region_9861 0 - +chr1 4643866 4643902 region_9863 0 - +chr1 4644097 4644133 region_9866 0 - +chr1 4644105 4644141 region_9867 0 - +chr1 4644703 4644739 region_9868 0 - +chr1 4645149 4645185 region_9872 0 - +chr1 4645237 4645273 region_9873 0 - +chr1 4645497 4645533 region_9875 0 - +chr1 4645690 4645726 region_9876 0 - +chr1 4645789 4645825 region_9877 0 - +chr1 4645969 4646005 region_9880 0 - +chr1 4646298 4646334 region_9884 0 - +chr1 4646461 4646497 region_9885 0 - +chr1 4646550 4646586 region_9887 0 - +chr1 4646719 4646755 region_9889 0 - +chr1 4646807 4646843 region_9891 0 - +chr1 4646879 4646915 region_9893 0 - +chr1 4646916 4646952 region_9894 0 - +chr1 4646987 4647023 region_9896 0 - +chr1 4647088 4647124 region_9898 0 - +chr1 4647559 4647595 region_9901 0 - +chr1 4647582 4647618 region_9902 0 - +chr1 4647696 4647732 region_9905 0 - +chr1 4648124 4648160 region_9908 0 - +chr1 4648129 4648165 region_9909 0 - +chr1 4648179 4648215 region_9910 0 - +chr1 4648523 4648559 region_9912 0 - +chr1 4648554 4648590 region_9914 0 - +chr1 4650119 4650155 region_9916 0 - +chr1 4650645 4650681 region_9917 0 - +chr1 4652025 4652061 region_9918 0 - +chr1 4652368 4652404 region_9921 0 - +chr1 4652487 4652523 region_9922 0 - +chr1 4652701 4652737 region_9924 0 - +chr1 4653073 4653109 region_9925 0 - +chr1 4653175 4653211 region_9926 0 - +chr1 4653199 4653235 region_9928 0 - +chr1 4653387 4653423 region_9931 0 - +chr1 4653471 4653507 region_9932 0 - +chr1 4653503 4653539 region_9933 0 - +chr1 4653574 4653610 region_9934 0 - +chr1 4656708 4656744 region_9938 0 - +chr1 4656721 4656757 region_9939 0 - +chr1 4656810 4656846 region_9941 0 - +chr1 4657008 4657044 region_9942 0 - +chr1 4657224 4657260 region_9943 0 - +chr1 4657590 4657626 region_9949 0 - +chr1 4657717 4657753 region_9950 0 - +chr1 4657724 4657760 region_9951 0 - +chr1 4657836 4657872 region_9953 0 - +chr1 4657909 4657945 region_9954 0 - +chr1 4657928 4657964 region_9956 0 - +chr1 4658311 4658347 region_9958 0 - +chr1 4658664 4658700 region_9963 0 - +chr1 4658713 4658749 region_9964 0 - +chr1 4658824 4658860 region_9965 0 - +chr1 4658866 4658902 region_9966 0 - +chr1 4658971 4659007 region_9969 0 - +chr1 4659035 4659071 region_9970 0 - +chr1 4659244 4659280 region_9971 0 - +chr1 4659465 4659501 region_9973 0 - +chr1 4659470 4659506 region_9974 0 - +chr1 4659504 4659540 region_9975 0 - +chr1 4659511 4659547 region_9977 0 - +chr1 4659530 4659566 region_9979 0 - +chr1 4659563 4659599 region_9980 0 - +chr1 4659578 4659614 region_9981 0 - +chr1 4659880 4659916 region_9986 0 - +chr1 4660125 4660161 region_9987 0 - +chr1 4660431 4660467 region_9991 0 - +chr1 4661557 4661593 region_9996 0 - +chr1 4661619 4661655 region_9997 0 - +chr1 4662104 4662140 region_9998 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/output_log_file.contains Mon Jan 27 09:28:33 2014 -0500 @@ -0,0 +1,287 @@ +############################################# +###### SICER v1.1 ###### +############################################# +Input library directory: +ChIP library: input_bed_file.bed +Control library: input_control_file.bed +Output directory: +Species: mm8 +Threshold for redundancy allowed for chip reads: 1 +Threshold for redundancy allowed for control reads: 1 +Window size: 200 bps +Fragment size: 150 bps. The shift for reads is half of 150 +Effective genome size as a fraction of the reference genome of mm8: 0.740000 +Gap size: 600 bps +Evalue for identification of candidate islands that exhibit clustering: 1000 +False discovery rate controlling significance: 0.01 +Preprocess the raw input_bed_file file to remove redundancy with threshold 1... +chr1 Plus reads: 4989 Retained plus reads: 4935 ; Minus reads: 5011 Retained minus reads: 4963 +chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +Preprocess the raw input_control_file file to remove redundancy with threshold 1... +chr1 Plus reads: 4980 Retained plus reads: 4937 ; Minus reads: 5020 Retained minus reads: 4959 +chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0 +Partion the genome in windows ... +Generate summary files ... +total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0 +total tag count in chr2.bed is: 0.0 = 0.0+0.0 +total tag count in chr3.bed is: 0.0 = 0.0+0.0 +total tag count in chr4.bed is: 0.0 = 0.0+0.0 +total tag count in chr5.bed is: 0.0 = 0.0+0.0 +total tag count in chr6.bed is: 0.0 = 0.0+0.0 +total tag count in chr7.bed is: 0.0 = 0.0+0.0 +total tag count in chr8.bed is: 0.0 = 0.0+0.0 +total tag count in chr9.bed is: 0.0 = 0.0+0.0 +total tag count in chr10.bed is: 0.0 = 0.0+0.0 +total tag count in chr11.bed is: 0.0 = 0.0+0.0 +total tag count in chr12.bed is: 0.0 = 0.0+0.0 +total tag count in chr13.bed is: 0.0 = 0.0+0.0 +total tag count in chr14.bed is: 0.0 = 0.0+0.0 +total tag count in chr15.bed is: 0.0 = 0.0+0.0 +total tag count in chr16.bed is: 0.0 = 0.0+0.0 +total tag count in chr17.bed is: 0.0 = 0.0+0.0 +total tag count in chr18.bed is: 0.0 = 0.0+0.0 +total tag count in chr19.bed is: 0.0 = 0.0+0.0 +total tag count in chrX.bed is: 0.0 = 0.0+0.0 +total tag count in chrY.bed is: 0.0 = 0.0+0.0 +total tag count in chrM.bed is: 0.0 = 0.0+0.0 +Normalize summary graph by total island filtered reads per million for input_bed_file ... +Convert the normalized summary graph into wig vstep format... +Find candidate islands exhibiting clustering ... +Species: mm8 +Window_size: 200 +Gap size: 600 +E value is: 1000.0 +Total read count: 9898.0 +Genome Length: 2644093988 +Effective genome Length: 1956629551 +Window average: 0.0010117398048 +Window pvalue: 0.2 +Minimum num of tags in a qualified window: 1 +Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows +Determine the score threshold from random background +The score threshold is: 6.898 +Make and write islands +Total number of islands: 417 +Calculate significance of candidate islands using the control library ... +chip library size 9898.0 +control library size 9896.0 +Total number of chip reads on islands is: 9811 +Total number of control reads on islands is: 8514 +Identify significant islands using FDR criterion ... +Given significance 0.01 , there are 184 significant islands +Convert island summary to island bed file of format chr start end ChIP-read-count +Filter reads with identified significant islands... +Make summary graph with filtered reads... +total tag count in chr1.bed is: 4303.0 = 2148.0+2155.0 +total tag count in chr2.bed is: 0.0 = 0.0+0.0 +total tag count in chr3.bed is: 0.0 = 0.0+0.0 +total tag count in chr4.bed is: 0.0 = 0.0+0.0 +total tag count in chr5.bed is: 0.0 = 0.0+0.0 +total tag count in chr6.bed is: 0.0 = 0.0+0.0 +total tag count in chr7.bed is: 0.0 = 0.0+0.0 +total tag count in chr8.bed is: 0.0 = 0.0+0.0 +total tag count in chr9.bed is: 0.0 = 0.0+0.0 +total tag count in chr10.bed is: 0.0 = 0.0+0.0 +total tag count in chr11.bed is: 0.0 = 0.0+0.0 +total tag count in chr12.bed is: 0.0 = 0.0+0.0 +total tag count in chr13.bed is: 0.0 = 0.0+0.0 +total tag count in chr14.bed is: 0.0 = 0.0+0.0 +total tag count in chr15.bed is: 0.0 = 0.0+0.0 +total tag count in chr16.bed is: 0.0 = 0.0+0.0 +total tag count in chr17.bed is: 0.0 = 0.0+0.0 +total tag count in chr18.bed is: 0.0 = 0.0+0.0 +total tag count in chr19.bed is: 0.0 = 0.0+0.0 +total tag count in chrX.bed is: 0.0 = 0.0+0.0 +total tag count in chrY.bed is: 0.0 = 0.0+0.0 +total tag count in chrM.bed is: 0.0 = 0.0+0.0 +Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million... +Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million... +Done! +Additionally, these warnings were reported: +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in +Warning: chr2 reads do not exist in +Warning: chr3 reads do not exist in +Warning: chr4 reads do not exist in +Warning: chr5 reads do not exist in +Warning: chr6 reads do not exist in +Warning: chr7 reads do not exist in +Warning: chr8 reads do not exist in +Warning: chr9 reads do not exist in +Warning: chr10 reads do not exist in +Warning: chr11 reads do not exist in +Warning: chr12 reads do not exist in +Warning: chr13 reads do not exist in +Warning: chr14 reads do not exist in +Warning: chr15 reads do not exist in +Warning: chr16 reads do not exist in +Warning: chr17 reads do not exist in +Warning: chr18 reads do not exist in +Warning: chr19 reads do not exist in +Warning: chrX reads do not exist in +Warning: chrY reads do not exist in +Warning: chrM reads do not exist in
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-1-removed.bed Mon Jan 27 09:28:33 2014 -0500 @@ -0,0 +1,9898 @@ +chr1 3002286 3002322 region_1 0 + +chr1 3002729 3002765 region_3 0 + +chr1 3002805 3002841 region_4 0 + +chr1 3003028 3003064 region_6 0 + +chr1 3003396 3003432 region_8 0 + +chr1 3003492 3003528 region_9 0 + +chr1 3004029 3004065 region_10 0 + +chr1 3004174 3004210 region_11 0 + +chr1 3004969 3005005 region_12 0 + +chr1 3005783 3005819 region_13 0 + +chr1 3017794 3017830 region_15 0 + +chr1 3018455 3018491 region_16 0 + +chr1 3018653 3018689 region_18 0 + +chr1 3018889 3018925 region_19 0 + +chr1 3019304 3019340 region_21 0 + +chr1 3019346 3019382 region_22 0 + +chr1 3019560 3019596 region_23 0 + +chr1 3019905 3019941 region_25 0 + +chr1 3020128 3020164 region_26 0 + +chr1 3020299 3020335 region_27 0 + +chr1 3020303 3020339 region_28 0 + +chr1 3020996 3021032 region_29 0 + +chr1 3021378 3021414 region_33 0 + +chr1 3022271 3022307 region_40 0 + +chr1 3023138 3023174 region_41 0 + +chr1 3023773 3023809 region_43 0 + +chr1 3025015 3025051 region_45 0 + +chr1 3027918 3027954 region_50 0 + +chr1 3028566 3028602 region_51 0 + +chr1 3028982 3029018 region_54 0 + +chr1 3035363 3035399 region_55 0 + +chr1 3035560 3035596 region_56 0 + +chr1 3035715 3035751 region_57 0 + +chr1 3035966 3036002 region_59 0 + +chr1 3037066 3037102 region_61 0 + +chr1 3037157 3037193 region_62 0 + +chr1 3037308 3037344 region_63 0 + +chr1 3038417 3038453 region_65 0 + +chr1 3038604 3038640 region_66 0 + +chr1 3038835 3038871 region_69 0 + +chr1 3038963 3038999 region_71 0 + +chr1 3039636 3039672 region_73 0 + +chr1 3039701 3039737 region_74 0 + +chr1 3040850 3040886 region_75 0 + +chr1 3041041 3041077 region_76 0 + +chr1 3041114 3041150 region_78 0 + +chr1 3051857 3051893 region_83 0 + +chr1 3052457 3052493 region_85 0 + +chr1 3052861 3052897 region_87 0 + +chr1 3053796 3053832 region_89 0 + +chr1 3054897 3054933 region_91 0 + +chr1 3054909 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peakcalling_sicer/test_2/test-W200-G600.scoreisland Mon Jan 27 09:28:33 2014 -0500 @@ -0,0 +1,417 @@ +chr1 3002000 3005999 92.4307844442 +chr1 3017800 3022399 188.155382275 +chr1 3023200 3023999 28.2805178042 +chr1 3026800 3029199 63.4581311992 +chr1 3035400 3039799 143.597790119 +chr1 3040800 3041999 43.8644449755 +chr1 3051600 3053999 55.8689001676 +chr1 3054800 3055999 51.4546877469 +chr1 3062200 3063999 70.3552267901 +chr1 3064800 3067199 56.9665007165 +chr1 3071000 3072199 36.2752139439 +chr1 3073400 3074199 27.5883823634 +chr1 3077400 3077599 14.4863266225 +chr1 3085600 3087199 120.793864279 +chr1 3088400 3088599 22.4810227622 +chr1 3089400 3089999 36.2752139439 +chr1 3091600 3091999 13.7941911817 +chr1 3092800 3093799 28.2805178042 +chr1 3094800 3095799 65.9400026296 +chr1 3104200 3105999 58.350771598 +chr1 3106800 3113599 327.445332228 +chr1 3114400 3115399 27.5883823634 +chr1 3117800 3124999 207.055921318 +chr1 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 27 09:28:33 2014 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="SICER" version="1.1"> + <repository changeset_revision="48c84c1cab2b" name="package_sicer_1_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>