# HG changeset patch
# User devteam
# Date 1390832913 18000
# Node ID 82a8234e03f289306e464d3fcde6ba202830d343
Imported from capsule None
diff -r 000000000000 -r 82a8234e03f2 sicer_wrapper.py
--- /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__()
diff -r 000000000000 -r 82a8234e03f2 sicer_wrapper.xml
--- /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 @@
+
+ Statistical approach for the Identification of ChIP-Enriched Regions
+ 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}"
+
+
+ SICER
+
+
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+ value is not None and value.dbkey in [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]
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+**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.*
+
+
+
diff -r 000000000000 -r 82a8234e03f2 test-data/chipseq_enriched.bed.gz
Binary file test-data/chipseq_enriched.bed.gz has changed
diff -r 000000000000 -r 82a8234e03f2 test-data/chipseq_input.bed.gz
Binary file test-data/chipseq_input.bed.gz has changed
diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/output_log_file.contains
--- /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
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+Warning: chr16 reads do not exist in
+Warning: chr17 reads do not exist in
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+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
diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-1-removed.bed
--- /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 @@
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered-normalized.wig Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_1/test-W200-G600-E0.01-islandfiltered.bed Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_1/test-W200.graph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_1/test-W200.graph Mon Jan 27 09:28:33 2014 -0500
@@ -0,0 +1,5667 @@
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/control-1-removed.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_2/control-1-removed.bed Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/output_log_file.contains
--- /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
diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-1-removed.bed
--- /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 @@
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-island.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered-normalized.wig Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_2/test-W200-G600-FDR0.01-islandfiltered.bed Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_2/test-W200-G600-islands-summary-FDR0.01 Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-G600.scoreisland
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200-normalized.wig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_2/test-W200-normalized.wig Mon Jan 27 09:28:33 2014 -0500
@@ -0,0 +1,5669 @@
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_2/test-W200.graph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_3/test-W200-G600-FDR0.01-island.bed Mon Jan 27 09:28:33 2014 -0500
@@ -0,0 +1,184 @@
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary Mon Jan 27 09:28:33 2014 -0500
@@ -0,0 +1,417 @@
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_3/test-W200-G600-islands-summary-FDR0.01 Mon Jan 27 09:28:33 2014 -0500
@@ -0,0 +1,184 @@
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200-G600.scoreisland
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_3/test-W200-G600.scoreisland Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_3/test-W200.graph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_3/test-W200.graph Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_4/test-W200-G600-E0.01.scoreisland
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 82a8234e03f2 test-data/peakcalling_sicer/test_4/test-W200.graph
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peakcalling_sicer/test_4/test-W200.graph Mon Jan 27 09:28:33 2014 -0500
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diff -r 000000000000 -r 82a8234e03f2 tool_dependencies.xml
--- /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 @@
+
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