Galaxy |

Changeset 2:1a6979fbd544 (2021-12-03)

Previous changeset 1:201d8e7dfc43 (2015-07-21)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/ccat commit 1370bb21ee5712a13a26d289065406c5d489b8cc"

modified:
ccat_wrapper.xml

added:
test-data/ES_CTCF_chr19.bed
test-data/ES_CTCF_chr19.log
test-data/ES_CTCF_chr19.significant.peak
test-data/ES_CTCF_chr19.significant.region
test-data/ES_CTCF_chr19.top100000.peak
test-data/ES_GFP_chr19.bed
test-data/ccat_configurations.loc
test-data/chipseq_enriched.bed
test-data/chipseq_input.bed
test-data/config_TF.txt
test-data/genome_length_mm8_chr19.txt
test-data/hg18.len
tool_data_table_conf.xml.test

diff -r 201d8e7dfc43 -r 1a6979fbd544 ccat_wrapper.py
--- a/ccat_wrapper.py Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

@@ -1,41 +0,0 @@
-import sys, subprocess, tempfile, shutil, os.path
-
-CCAT_BINARY = "CCAT"
-
-def get_top_count( filename ):
-    for line in open( filename ):
-        if line.startswith( 'outputNum' ):
-            return int( line.split()[-1].strip() )
-
-def stop_err( tmp_dir, exception ):
-    print >> sys.stderr, "Error running CCAT."
-    shutil.rmtree( tmp_dir ) #some error has occurred, provide info and remove possibly non-empty temp directory
-    raise exception
-
-def main():
-    input_tag_file = sys.argv[1]
-    input_control_file = sys.argv[2]
-    chrom_info_file = sys.argv[3]
-    input_config_file = sys.argv[4]
-    project_name = sys.argv[5]
-    output_peak_file = sys.argv[6]
-    output_region_file = sys.argv[7]
-    output_top_file = sys.argv[8]
-    output_log_file = sys.argv[9]
-
-    tmp_dir = tempfile.mkdtemp()
-    try:
-        assert os.path.exists( chrom_info_file ), "The required chromosome length file does not exist."
-        proc = subprocess.Popen( args="%s %s > %s" % ( CCAT_BINARY, " ".join( map( lambda x: "'%s'" % x, [ input_tag_file, input_control_file, chrom_info_file, input_config_file, project_name ] ) ), output_log_file ), shell=True, cwd=tmp_dir )
-        proc.wait()
-        if proc.returncode:
-            raise Exception( "Error code: %i" % proc.returncode )
-        output_num = get_top_count( input_config_file )
-        shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file )
-        shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file )
-        shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file )
-    except Exception, e:
-        return stop_err( tmp_dir, e )
-    os.rmdir( tmp_dir ) #clean up empty temp working directory
-
-if __name__ == "__main__": main()

diff -r 201d8e7dfc43 -r 1a6979fbd544 ccat_wrapper.xml
--- a/ccat_wrapper.xml Tue Jul 21 14:13:34 2015 -0400
+++ b/ccat_wrapper.xml Fri Dec 03 16:27:57 2021 +0000

[

b'@@ -1,23 +1,49 @@\n-<tool id="peakcalling_ccat" name="CCAT" version="0.0.1">\n+<tool id="peakcalling_ccat" name="CCAT" version="0.0.2" profile="20.01">\n <description>Control-based ChIP-seq Analysis Tool</description>\n <requirements>\n- <requirement type="package" version="3.0">CCAT</requirement>\n+ <requirement type="package" version="3.0">ccat</requirement>\n </requirements>\n- <command interpreter="python">ccat_wrapper.py \'$input_tag_file\' \'$input_control_file\' \'$chromInfo\' \n- #if str( $options_type[ \'options_type_selector\' ] ) == \'advanced\':\n- \'$input_advanced_config_file\' \n- #else:\n- \'${ options_type.input_config_file.fields.path }\'\n- #end if\n- \'CCAT in Galaxy\' \n- \'$output_peak_file\' \'$output_region_file\' \'$output_top_file\' \'$output_log_file\'</command>\n+ <stdio>\n+ <regex match="Usage: <library 1 tag file name> <library 2 tag file name> <chromosome length file name> <config file name> <project name>"\n+ source="both"\n+ level="fatal"\n+ description="CLI error" />\n+ <regex match="tag file error" source="both" level="fatal" description="tag file error" />\n+ </stdio>\n+ <command detect_errors="aggressive"><![CDATA[\n+ echo $in_test_mode && CCAT \'$input_tag_file\'\n+ \'$input_control_file\'\n+ #if str($in_test_mode) == "no":\n+ \'$chromInfo\'\n+ #else:\n+ \'$__tool_directory__/test-data/genome_length_mm8_chr19.txt\'\n+ #end if\n+ #if str($options_type[\'options_type_selector\']) == \'advanced\':\n+ \'$input_advanced_config_file\' \n+ #else:\n+ \'${options_type.input_config_file.fields.path}\'\n+ #end if\n+ CCAT\n+ | tee \'$output_log_file\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="input_advanced_config_file"><![CDATA[\n+#if str($options_type[\'options_type_selector\']) == \'advanced\':\n+fragmentSize\t${options_type[\'fragment_size\']}\n+slidingWinSize\t${options_type[\'sliding_window_size\']}\n+movingStep\t${options_type[\'moving_step\']}\n+isStrandSensitiveMode\t${options_type[\'is_strand_sensitive_mode\']}\n+minCount\t${options_type[\'min_count\']}\n+outputNum\t${options_type[\'output_num\']}\n+randomSeed\t${options_type[\'random_seed\']}\n+minScore\t${options_type[\'min_score\']}\t\n+bootstrapPass\t${options_type[\'bootstrap_pass\']}\n+#end if\n+ ]]></configfile>\n+ </configfiles>\n <inputs>\n- <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" >\n- <validator type="unspecified_build" />\n- </param>\n- <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" >\n- <validator type="unspecified_build" />\n- </param>\n+ <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File"/>\n+ <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File"/>\n <conditional name="options_type">\n <param name="options_type_selector" type="select" label="Advanced Options">\n <option value="basic" selected="True">Hide Advanced Options</option>\n@@ -45,23 +71,24 @@\n <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>\n </when>\n </conditional>\n+ <param name="in_test_mode" type="hidden" value="no" />\n </inputs>\n <outputs>\n- <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">\n+ <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)" from_work_dir="CCAT.significant.peak">\n <actions>\n <action type="metadata" name="chromCol" default="1"/>\n <action type="metadata" name="startCol" default="3"/>\n <action type="metadata" name="endCol" default="4"/>\n </actions>\n </data>\n- <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">\n+ <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)" from_work_dir="CCAT.significant.region">\n '..b'ram name="bootstrap_pass" value="50" />\n- <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />\n- <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />\n- <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" />\n- <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />\n+ <param name="in_test_mode" value="yes" />\n+ <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak"/>\n+ <output name="output_region_file" file="ES_CTCF_chr19.significant.region" />\n+ <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" />\n+ <output name="output_log_file" file="ES_CTCF_chr19.log" />\n </test>\n <test>\n- <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />\n- <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />\n+ <param name="input_tag_file" value="ES_CTCF_chr19.bed" ftype="bed" dbkey="hg18" />\n+ <param name="input_control_file" value="ES_GFP_chr19.bed" ftype="bed" dbkey="hg18" />\n <param name="options_type_selector" value="basic" />\n- <param name="input_config_file" value="ccat_3.0_histone_config" />\n- <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />\n- <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />\n- <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />\n- <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />\n+ <param name="input_config_file" value="config_TF" />\n+ <param name="in_test_mode" value="yes" />\n+ <output name="output_peak_file" file="ES_CTCF_chr19.significant.peak" />\n+ <output name="output_region_file" file="ES_CTCF_chr19.significant.region" />\n+ <output name="output_top_file" file="ES_CTCF_chr19.top100000.peak" />\n+ <output name="output_log_file" file="ES_CTCF_chr19.log" />\n </test>\n- \n- \n </tests>\n <help>\n **What it does**\n \n This tool allows ChIP-seq peak/region calling using CCAT.\n \n-View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm.\n-\n-------\n-\n-**Citation**\n-\n-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*\n-\n+View the original CCAT documentation: https://www.comp.nus.edu.sg/~bioinfo/CCAT3.0/\n </help>\n <citations>\n <citation type="doi">10.1093/bioinformatics/btq128</citation>\n'

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/1.interval
--- a/test-data/1.interval Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,5 +0,0 @@
-chr1 4348187 4348589 3.70 4.90 2.55 0.24 0.46
-chr1 4488177 4488442 4.03 5.77 1.92 -0.67 0.81
-chr1 4774091 4774440 8.07 8.33 7.82 0.85 -0.40
-chr1 4800122 4800409 6.40 7.35 5.44 1.19 -0.42
-chr1 4878925 4879277 2.18 0.28 4.93 -0.96 1.24

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/1.txt
--- a/test-data/1.txt Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,10 +0,0 @@
-chr1    4225    19670
-chr10   6       8
-chr1    24417   24420
-chr6_hla_hap2   0       150
-chr2    1       5
-chr10   2       10
-chr1    30      55
-chrY    1       20
-chr1    1225979 42287290
-chr10   7       8

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/2.interval
--- a/test-data/2.interval Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,14 +0,0 @@
-chrX 151117436 151117437 + 0.14351
-chrX 151117437 151117438 + 0.139843
-chrX 151117438 151117439 + 0.132509
-chrX 151117439 151117440 + 0.139843
-chrX 151117440 151117441 + 0.169179
-chrX 151117441 151117442 + 0.257185
-chrX 151117442 151117443 + 0.319523
-chrX 151117443 151117444 + 0.367193
-chrX 151117444 151117445 + 0.400195
-chrX 151117445 151117446 + 0.425864
-chrX 151117446 151117447 + 0.444198
-chrX 151117447 151117448 + 0.455199
-chrX 151117448 151117449 + 0.462533
-chrX 151117449 151117450 + 0.4662

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/2.txt
--- a/test-data/2.txt Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
-chr1    4225    19670
-chr10   6       8
-chr1    24417   24420
-chr6_hla_hap2   0       150
-chr2    1       5
-chr1    30      55
-chrY    1       20
-chr1    1225979 42287290

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ES_CTCF_chr19.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_CTCF_chr19.bed Fri Dec 03 16:27:57 2021 +0000

b'@@ -0,0 +1,103146 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diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ES_CTCF_chr19.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_CTCF_chr19.log Fri Dec 03 16:27:57 2021 +0000

@@ -0,0 +1,53 @@
+chromosome length information read. chromNum = 1!
+config file read.
+fragmentSize = 200
+isStrandSensitiveMode = 1
+slidingWinSize = 300
+movingStep = 10
+outputNum = 100000
+minCount = 3
+minScore = 5.000000
+bootstrapPass = 50
+randSeed = 123456
+reading tag files......
+103146 tags in L1, 97149 tags in L2.
+tag file read.
+pre-processing......
+pre-processing finished.
+estimating noise rate......
+iteration 0: nr=0.669578
+iteration 1: nr=0.613605
+iteration 2: nr=0.593059
+iteration 3: nr=0.586303
+iteration 4: nr=0.583061
+iteration 5: nr=0.583061
+iteration 6: nr=0.582451
+iteration 7: nr=0.586573
+iteration 8: nr=0.583271
+iteration 9: nr=0.581424
+iteration 10: nr=0.585253
+iteration 11: nr=0.583917
+iteration 12: nr=0.583446
+iteration 13: nr=0.581896
+iteration 14: nr=0.583084
+iteration 15: nr=0.581582
+iteration 16: nr=0.582966
+iteration 17: nr=0.583596
+iteration 18: nr=0.586691
+iteration 19: nr=0.584954
+noise rate = 0.583743
+peak-finding......
+chr19......2946 candidate peaks.
+peak-finding finished.
+Significance Analysis......
+estimating paramters......
+smoothing factor = 20.048787
+estimating local FDR.....
+FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files.
+post-processing......
+chr19......finished.
+post-processing finished.
+Significance analysis finished.
+saving results.......
+results saved.
+CCAT process completed!

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ES_CTCF_chr19.significant.peak
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_CTCF_chr19.significant.peak Fri Dec 03 16:27:57 2021 +0000

b'@@ -0,0 +1,2946 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5013330\t3\t2\t6.047518\t0.957000\n+chr19\t11178425\t11178200\t11178700\t3\t2\t6.047518\t0.957000\n+chr19\t44860265\t44860060\t44860520\t3\t2\t6.047518\t0.957000\n+chr19\t32670135\t32669900\t32670370\t3\t2\t6.047518\t0.957000\n+chr19\t58258095\t58257860\t58258330\t3\t2\t6.047518\t0.957000\n+chr19\t35750885\t35750670\t35751100\t3\t2\t6.047518\t0.957000\n+chr19\t53789135\t53787970\t53789400\t3\t2\t6.047518\t0.957000\n+chr19\t19143895\t19143670\t19144160\t3\t2\t6.047518\t0.957000\n+chr19\t19293905\t19293650\t19294160\t3\t2\t6.047518\t0.957000\n+chr19\t18908575\t18908270\t18908810\t3\t2\t6.047518\t0.957000\n+chr19\t32313225\t32313070\t32313490\t3\t2\t6.047518\t0.957000\n+chr19\t43692155\t43691940\t43692360\t3\t2\t6.047518\t0.957000\n+chr19\t21607175\t21606920\t21607430\t3\t2\t6.047518\t0.957000\n+chr19\t21656405\t21656220\t21656700\t3\t2\t6.047518\t0.957000\n+chr19\t43676495\t43676210\t43676750\t3\t2\t6.047518\t0.957000\n+chr19\t57602135\t57601860\t57602370\t3\t2\t6.047518\t0.957000\n+chr19\t18690945\t18690750\t18691170\t3\t2\t6.047518\t0.957000\n+chr19\t57813175\t57812920\t57813440\t3\t2\t6.047518\t0.957000\n+chr19\t32535125\t32534860\t32535380\t3\t2\t6.047518\t0.957000\n+chr19\t37741795\t37741570\t37742080\t3\t2\t6.047518\t0.957000\n+chr19\t18256375\t18256160\t18256590\t3\t2\t6.047518\t0.957000\n+chr19\t43937585\t43937330\t43937910\t3\t2\t6.047518\t0.957000\n+chr19\t47233545\t47233090\t47233700\t3\t3\t5.918914\t0.957000\n+chr19\t38193265\t38192990\t38193430\t3\t3\t5.918914\t0.957000\n+chr19\t3951425\t3950700\t3951660\t3\t3\t5.918914\t0.957000\n+chr19\t47546645\t47546330\t47547000\t3\t3\t5.918914\t0.957000\n+chr19\t4278415\t4278130\t4278700\t3\t3\t5.918914\t0.957000\n+chr19\t4723155\t4722920\t4723390\t3\t3\t5.918914\t0.957000\n+chr19\t47756715\t47756520\t47757010\t3\t3\t5.918914\t0.957000\n+chr19\t36971365\t36971090\t36971640\t3\t3\t5.918914\t0.957000\n+chr19\t34085305\t34085040\t34085500\t3\t3\t5.918914\t0.957000\n+chr19\t6928335\t6928000\t6928610\t3\t3\t5.918914\t0.957000\n+chr19\t20044205\t20043840\t20044450\t3\t3\t5.918914\t0.957000\n+chr19\t43729605\t43729380\t43729820\t3\t3\t5.918914\t0.957000\n+chr19\t46607255\t46607000\t46607510\t3\t3\t5.918914\t0.957000\n+chr19\t23761625\t23761440\t23761880\t3\t3\t5.918914\t0.957000\n+chr19\t42796325\t42796090\t42796550\t3\t3\t5.918914\t0.957000\n+chr19\t43962235\t43961990\t43962570\t3\t3\t5.918914\t0.957000\n+chr19\t10212245\t10212080\t10212550\t3\t3\t5.918914\t0.957000\n+chr19\t15367425\t15367150\t15367610\t3\t3\t5.918914\t0.957000\n+chr19\t10862305\t10862020\t10862470\t3\t3\t5.918914\t0.957000\n+chr19\t9020905\t9020740\t9021160\t3\t3\t5.918914\t0.957000\n+chr19\t53609775\t53609560\t53610700\t3\t3\t5.918914\t0.957000\n+chr19\t44325745\t44325380\t44325970\t3\t3\t5.918914\t0.957000\n+chr19\t57050495\t57050270\t57051030\t3\t3\t5.918914\t0.957000\n+chr19\t41794715\t41794430\t41795000\t3\t3\t5.918914\t0.957000\n+chr19\t46861375\t46861180\t46861650\t3\t3\t5.918914\t0.957000\n+chr19\t26644885\t26644630\t26645130\t3\t3\t5.918914\t0.957000\n+chr19\t41123325\t41123110\t41123530\t3\t3\t5.918914\t0.957000\n+chr19\t47066795\t47065600\t47067050\t3\t3\t5.918914\t0.957000\n+chr19\t5858385\t5858080\t5858680\t3\t3\t5.918914\t0.957000\n+chr19\t42348215\t42347860\t42348430\t3\t3\t5.918914\t0.957000\n+chr19\t6263805\t6263530\t6263970\t3\t3\t5.918914\t0.957000\n+chr19\t46696705\t46696480\t46696930\t3\t3\t5.918914\t0.957000\n+chr19\t5884865\t5884560\t5885170\t3\t3\t5.918914\t0.957000\n+chr19\t57177075\t57176800\t57177340\t3\t3\t5.918914\t0.957000\n+chr19\t24722775\t24722470\t24723010\t3\t3\t5.918914\t0.957000\n+chr19\t21851155\t21850910\t21851340\t3\t4\t5.752407\t1.000000\n+chr19\t53306355\t53306120\t53306590\t3\t4\t5.752407\t1.000000\n+chr19\t44909225\t44908970\t44909480\t3\t4\t5.752407\t1.000000\n+chr19\t43643065\t43642820\t43643310\t3\t4\t5.752407\t1.000000\n+chr19\t47496375\t47496160\t47496590\t3\t4\t5.752407\t1.000000\n+chr19\t37642155\t37641960\t37642440\t3\t4\t5.752407\t1.000000\n+chr19\t25418055\t25417860\t25418400\t3\t4\t5.752407\t1.000000\n+chr19\t28974665\t28974450\t28974870\t3\t4\t5.752407\t1.000000\n'

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ES_CTCF_chr19.significant.region
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_CTCF_chr19.significant.region Fri Dec 03 16:27:57 2021 +0000

b'@@ -0,0 +1,2808 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4225\t29334060\t29334510\t3\t2\t6.047518\t0.957000\n+chr19\t47146745\t47146460\t47147020\t3\t2\t6.047518\t0.957000\n+chr19\t7680375\t7680080\t7680760\t3\t2\t6.047518\t0.957000\n+chr19\t24074745\t24074560\t24075040\t3\t2\t6.047518\t0.957000\n+chr19\t45196965\t45196680\t45197240\t3\t2\t6.047518\t0.957000\n+chr19\t7479015\t7478800\t7479230\t3\t2\t6.047518\t0.957000\n+chr19\t24068055\t24067790\t24068240\t3\t2\t6.047518\t0.957000\n+chr19\t6022535\t6022300\t6022710\t3\t2\t6.047518\t0.957000\n+chr19\t7523955\t7523680\t7524290\t3\t2\t6.047518\t0.957000\n+chr19\t25375995\t25375730\t25376160\t3\t2\t6.047518\t0.957000\n+chr19\t58258095\t58257860\t58258330\t3\t2\t6.047518\t0.957000\n+chr19\t26155595\t26155340\t26155900\t3\t2\t6.047518\t0.957000\n+chr19\t46894095\t46893810\t46894370\t3\t2\t6.047518\t0.957000\n+chr19\t46847875\t46847640\t46848110\t3\t2\t6.047518\t0.957000\n+chr19\t25164845\t25164530\t25165130\t3\t2\t6.047518\t0.957000\n+chr19\t8624545\t8624300\t8624730\t3\t2\t6.047518\t0.957000\n+chr19\t36168545\t36168380\t36168830\t3\t2\t6.047518\t0.957000\n+chr19\t40783205\t40783020\t40783490\t3\t2\t6.047518\t0.957000\n+chr19\t47206905\t47206700\t47207270\t3\t2\t6.047518\t0.957000\n+chr19\t57813175\t57812920\t57813440\t3\t2\t6.047518\t0.957000\n+chr19\t38174335\t38174020\t38174590\t3\t2\t6.047518\t0.957000\n+chr19\t29660965\t29660680\t29661240\t3\t2\t6.047518\t0.957000\n+chr19\t45449465\t45449250\t45449680\t3\t2\t6.047518\t0.957000\n+chr19\t55604645\t55604380\t55604910\t3\t2\t6.047518\t0.957000\n+chr19\t4605345\t4605090\t4605650\t3\t2\t6.047518\t0.957000\n+chr19\t42348215\t42347860\t42348430\t3\t3\t5.918914\t0.957000\n+chr19\t20044205\t20043840\t20044450\t3\t3\t5.918914\t0.957000\n+chr19\t10212245\t10212080\t10212550\t3\t3\t5.918914\t0.957000\n+chr19\t47233545\t47233090\t47233700\t3\t3\t5.918914\t0.957000\n+chr19\t46607255\t46607000\t46607510\t3\t3\t5.918914\t0.957000\n+chr19\t46861375\t46861180\t46861650\t3\t3\t5.918914\t0.957000\n+chr19\t42796325\t42796090\t42796550\t3\t3\t5.918914\t0.957000\n+chr19\t46696705\t46696480\t46696930\t3\t3\t5.918914\t0.957000\n+chr19\t5884865\t5884560\t5885170\t3\t3\t5.918914\t0.957000\n+chr19\t38193265\t38192990\t38193430\t3\t3\t5.918914\t0.957000\n+chr19\t4723155\t4722920\t4723390\t3\t3\t5.918914\t0.957000\n+chr19\t5858385\t5858080\t5858680\t3\t3\t5.918914\t0.957000\n+chr19\t36971365\t36971090\t36971640\t3\t3\t5.918914\t0.957000\n+chr19\t34085305\t34085040\t34085500\t3\t3\t5.918914\t0.957000\n+chr19\t47546645\t47546330\t47547000\t3\t3\t5.918914\t0.957000\n+chr19\t41123325\t41123110\t41123530\t3\t3\t5.918914\t0.957000\n+chr19\t4278415\t4278130\t4278700\t3\t3\t5.918914\t0.957000\n+chr19\t15367425\t15367150\t15367610\t3\t3\t5.918914\t0.957000\n+chr19\t23761625\t23761440\t23761880\t3\t3\t5.918914\t0.957000\n+chr19\t47756715\t47756520\t47757010\t3\t3\t5.918914\t0.957000\n+chr19\t41794715\t41794430\t41795000\t3\t3\t5.918914\t0.957000\n+chr19\t26644885\t26644630\t26645130\t3\t3\t5.918914\t0.957000\n+chr19\t44325745\t44325380\t44325970\t3\t3\t5.918914\t0.957000\n+chr19\t10862305\t10862020\t10862470\t3\t3\t5.918914\t0.957000\n+chr19\t57177075\t57176800\t57177340\t3\t3\t5.918914\t0.957000\n+chr19\t43962235\t43961990\t43962570\t3\t3\t5.918914\t0.957000\n+chr19\t43729605\t43729380\t43729820\t3\t3\t5.918914\t0.957000\n+chr19\t6263805\t6263530\t6263970\t3\t3\t5.918914\t0.957000\n+chr19\t57050495\t57050270\t57051030\t3\t3\t5.918914\t0.957000\n+chr19\t24722775\t24722470\t24723010\t3\t3\t5.918914\t0.957000\n+chr19\t9020905\t9020740\t9021160\t3\t3\t5.918914\t0.957000\n+chr19\t6928335\t6928000\t6928610\t3\t3\t5.918914\t0.957000\n+chr19\t47496375\t47496160\t47496590\t3\t4\t5.752407\t1.000000\n+chr19\t44909225\t44908970\t44909480\t3\t4\t5.752407\t1.000000\n+chr19\t53306355\t53306120\t53306590\t3\t4\t5.752407\t1.000000\n+chr19\t21851155\t21850910\t21851340\t3\t4\t5.752407\t1.000000\n+chr19\t43643065\t43642820\t43643310\t3\t4\t5.752407\t1.000000\n+chr19\t37642155\t37641960\t37642440\t3\t4\t5.752407\t1.000000\n+chr19\t28974665\t28974450\t28974870\t3\t4\t5.752407\t1.000000\n+chr19\t25418055\t25417860\t25418400\t3\t4\t5.752407\t1.000000\n'

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ES_CTCF_chr19.top100000.peak
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_CTCF_chr19.top100000.peak Fri Dec 03 16:27:57 2021 +0000

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ES_GFP_chr19.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ES_GFP_chr19.bed Fri Dec 03 16:27:57 2021 +0000

b'@@ -0,0 +1,97149 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diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/a.tab
--- a/test-data/a.tab Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,15 +0,0 @@
-CHR SNP BP A1 TEST NMISS BETA STAT P
-1 rs1181876 3671541 T DOMDEV 958 -1.415 -3.326 0.0009161
-1 rs10492923 5092886 C ADD 1007 5.105 4.368 1.382e-05
-1 rs10492923 5092886 C DOMDEV 1007 -5.612 -4.249 2.35e-05
-1 rs10492923 5092886 C GENO_2DF 1007 NA 19.9 4.775e-05
-1 rs1801133 11778965 T ADD 1022 1.23 3.97 7.682e-05
-1 rs1801133 11778965 T GENO_2DF 1022 NA 16.07 0.0003233
-1 rs1361912 12663121 A ADD 1021 12.69 4.093 4.596e-05
-1 rs1361912 12663121 A DOMDEV 1021 -12.37 -3.945 8.533e-05
-1 rs1361912 12663121 A GENO_2DF 1021 NA 17.05 0.0001982
-1 rs1009806 19373138 G ADD 1021 -1.334 -3.756 0.0001826
-1 rs1009806 19373138 G GENO_2DF 1021 NA 19.36 6.244e-05
-1 rs873654 29550948 A DOMDEV 1012 1.526 3.6 0.0003339
-1 rs10489527 36800027 C ADD 1016 12.67 4.114 4.211e-05
-1 rs10489527 36800027 C DOMDEV 1016 -13.05 -4.02 6.249e-05

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/ccat_configurations.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ccat_configurations.loc Fri Dec 03 16:27:57 2021 +0000

@@ -0,0 +1,1 @@
+config_TF config_TF ${__HERE__}/config_TF.txt

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/chipseq_enriched.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chipseq_enriched.bed Fri Dec 03 16:27:57 2021 +0000

b'@@ -0,0 +1,10000 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diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/chipseq_enriched.bed.gz

Binary file test-data/chipseq_enriched.bed.gz has changed

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/chipseq_input.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chipseq_input.bed Fri Dec 03 16:27:57 2021 +0000

b'@@ -0,0 +1,10000 @@\n+chr1\t3001825\t3001861\tregion_0\t0\t-\n+chr1\t3002334\t3002370\tregion_1\t0\t+\n+chr1\t3002376\t3002412\tregion_2\t0\t+\n+chr1\t3002409\t3002445\tregion_3\t0\t+\n+chr1\t3002513\t3002549\tregion_4\t0\t-\n+chr1\t3002530\t3002566\tregion_5\t0\t-\n+chr1\t3002773\t3002809\tregion_6\t0\t+\n+chr1\t3002826\t3002862\tregion_7\t0\t-\n+chr1\t3002837\t3002873\tregion_8\t0\t-\n+chr1\t3003123\t3003159\tregion_9\t0\t-\n+chr1\t3003136\t3003172\tregion_10\t0\t+\n+chr1\t3003183\t3003219\tregion_11\t0\t+\n+chr1\t3003548\t3003584\tregion_12\t0\t-\n+chr1\t3003699\t3003735\tregion_13\t0\t+\n+chr1\t3003700\t3003736\tregion_14\t0\t+\n+chr1\t3003806\t3003842\tregion_15\t0\t-\n+chr1\t3003807\t3003843\tregion_16\t0\t-\n+chr1\t3003871\t3003907\tregion_17\t0\t-\n+chr1\t3004112\t3004148\tregion_18\t0\t-\n+chr1\t3004263\t3004299\tregion_19\t0\t+\n+chr1\t3004503\t3004539\tregion_20\t0\t+\n+chr1\t3005056\t3005092\tregion_21\t0\t-\n+chr1\t3005109\t3005145\tregion_22\t0\t+\n+chr1\t3005814\t3005850\tregion_23\t0\t+\n+chr1\t3012338\t3012374\tregion_24\t0\t+\n+chr1\t3012362\t3012398\tregion_25\t0\t+\n+chr1\t3012639\t3012675\tregion_26\t0\t+\n+chr1\t3012707\t3012743\tregion_27\t0\t-\n+chr1\t3012924\t3012960\tregion_28\t0\t+\n+chr1\t3013931\t3013967\tregion_29\t0\t+\n+chr1\t3014180\t3014216\tregion_30\t0\t+\n+chr1\t3015798\t3015834\tregion_31\t0\t-\n+chr1\t3017021\t3017057\tregion_32\t0\t+\n+chr1\t3017070\t3017106\tregion_33\t0\t+\n+chr1\t3017705\t3017741\tregion_34\t0\t+\n+chr1\t3017714\t3017750\tregion_35\t0\t-\n+chr1\t3017719\t3017755\tregion_36\t0\t-\n+chr1\t3018632\t3018668\tregion_37\t0\t-\n+chr1\t3018651\t3018687\tregion_38\t0\t+\n+chr1\t3018685\t3018721\tregion_39\t0\t+\n+chr1\t3018749\t3018785\tregion_40\t0\t+\n+chr1\t3018763\t3018799\tregion_41\t0\t-\n+chr1\t3018845\t3018881\tregion_42\t0\t+\n+chr1\t3019016\t3019052\tregion_43\t0\t+\n+chr1\t3019056\t3019092\tregion_44\t0\t-\n+chr1\t3019198\t3019234\tregion_45\t0\t-\n+chr1\t3019245\t3019281\tregion_46\t0\t-\n+chr1\t3019424\t3019460\tregion_47\t0\t+\n+chr1\t3019503\t3019539\tregion_48\t0\t+\n+chr1\t3019573\t3019609\tregion_49\t0\t+\n+chr1\t3019649\t3019685\tregion_50\t0\t+\n+chr1\t3019825\t3019861\tregion_51\t0\t-\n+chr1\t3019842\t3019878\tregion_52\t0\t+\n+chr1\t3019908\t3019944\tregion_53\t0\t+\n+chr1\t3020099\t3020135\tregion_54\t0\t+\n+chr1\t3020099\t3020135\tregion_55\t0\t-\n+chr1\t3020410\t3020446\tregion_56\t0\t+\n+chr1\t3020436\t3020472\tregion_57\t0\t+\n+chr1\t3020506\t3020542\tregion_58\t0\t-\n+chr1\t3020632\t3020668\tregion_59\t0\t+\n+chr1\t3021163\t3021199\tregion_60\t0\t+\n+chr1\t3021168\t3021204\tregion_61\t0\t-\n+chr1\t3021171\t3021207\tregion_62\t0\t+\n+chr1\t3021200\t3021236\tregion_63\t0\t+\n+chr1\t3021290\t3021326\tregion_64\t0\t-\n+chr1\t3021351\t3021387\tregion_65\t0\t-\n+chr1\t3021760\t3021796\tregion_66\t0\t-\n+chr1\t3021769\t3021805\tregion_67\t0\t+\n+chr1\t3021769\t3021805\tregion_68\t0\t-\n+chr1\t3022550\t3022586\tregion_69\t0\t-\n+chr1\t3022597\t3022633\tregion_70\t0\t-\n+chr1\t3022609\t3022645\tregion_71\t0\t+\n+chr1\t3024825\t3024861\tregion_72\t0\t-\n+chr1\t3025035\t3025071\tregion_73\t0\t-\n+chr1\t3026253\t3026289\tregion_74\t0\t+\n+chr1\t3026835\t3026871\tregion_75\t0\t+\n+chr1\t3026950\t3026986\tregion_76\t0\t-\n+chr1\t3027203\t3027239\tregion_77\t0\t+\n+chr1\t3027273\t3027309\tregion_78\t0\t-\n+chr1\t3028473\t3028509\tregion_79\t0\t-\n+chr1\t3028648\t3028684\tregion_80\t0\t-\n+chr1\t3035392\t3035428\tregion_81\t0\t+\n+chr1\t3035417\t3035453\tregion_82\t0\t+\n+chr1\t3035533\t3035569\tregion_83\t0\t-\n+chr1\t3035631\t3035667\tregion_84\t0\t+\n+chr1\t3035745\t3035781\tregion_85\t0\t+\n+chr1\t3035812\t3035848\tregion_86\t0\t-\n+chr1\t3035953\t3035989\tregion_87\t0\t+\n+chr1\t3036879\t3036915\tregion_88\t0\t+\n+chr1\t3036895\t3036931\tregion_89\t0\t+\n+chr1\t3036895\t3036931\tregion_90\t0\t+\n+chr1\t3036932\t3036968\tregion_91\t0\t-\n+chr1\t3037005\t3037041\tregion_92\t0\t+\n+chr1\t3037005\t3037041\tregion_93\t0\t-\n+chr1\t3037056\t3037092\tregion_94\t0\t+\n+chr1\t3037424\t3037460\tregion_95\t0\t+\n+chr1\t3037433\t3037469\tregion_96\t0\t+\n+chr1\t3037588\t3037624\tregion_97\t0\t+\n+chr1\t3037807\t3037843\tregion_98\t0\t+\n+chr1\t3038118\t3038154\tregion_99\t0\t-\n+chr1\t3038427\t3038463\tregion_100\t0\t-\n+chr1\t3038447\t3038483\tregion_101\t0\t+\n+chr1\t3038498\t3038534\tregion_102\t0\t-\n+chr1\t3038557\t3038593\tregion_103\t0\t-\n+chr1\t3038631\t3038667\tregion_104\t0\t+\n+chr1\t3038670\t3038706\tregion_105\t0\t+\n+chr1\t3038775\t3038811\tregion_106\t0\t+\n+chr1\t3038786\t3038822\tregion_107\t0\t+\n+chr1\t3038794\t3038830\tregion_108\t0\t-\n+chr1\t3039016\t3039052\tregion_109\t0\t+\n+chr1\t3039031\t30390'..b'9894\t0\t-\n+chr1\t4646928\t4646964\tregion_9895\t0\t+\n+chr1\t4646987\t4647023\tregion_9896\t0\t-\n+chr1\t4647000\t4647036\tregion_9897\t0\t+\n+chr1\t4647088\t4647124\tregion_9898\t0\t-\n+chr1\t4647181\t4647217\tregion_9899\t0\t+\n+chr1\t4647281\t4647317\tregion_9900\t0\t+\n+chr1\t4647559\t4647595\tregion_9901\t0\t-\n+chr1\t4647582\t4647618\tregion_9902\t0\t-\n+chr1\t4647591\t4647627\tregion_9903\t0\t+\n+chr1\t4647654\t4647690\tregion_9904\t0\t+\n+chr1\t4647696\t4647732\tregion_9905\t0\t-\n+chr1\t4647722\t4647758\tregion_9906\t0\t+\n+chr1\t4647755\t4647791\tregion_9907\t0\t+\n+chr1\t4648124\t4648160\tregion_9908\t0\t-\n+chr1\t4648129\t4648165\tregion_9909\t0\t-\n+chr1\t4648179\t4648215\tregion_9910\t0\t-\n+chr1\t4648461\t4648497\tregion_9911\t0\t+\n+chr1\t4648523\t4648559\tregion_9912\t0\t-\n+chr1\t4648532\t4648568\tregion_9913\t0\t+\n+chr1\t4648554\t4648590\tregion_9914\t0\t-\n+chr1\t4650071\t4650107\tregion_9915\t0\t+\n+chr1\t4650119\t4650155\tregion_9916\t0\t-\n+chr1\t4650645\t4650681\tregion_9917\t0\t-\n+chr1\t4652025\t4652061\tregion_9918\t0\t-\n+chr1\t4652316\t4652352\tregion_9919\t0\t+\n+chr1\t4652334\t4652370\tregion_9920\t0\t+\n+chr1\t4652368\t4652404\tregion_9921\t0\t-\n+chr1\t4652487\t4652523\tregion_9922\t0\t-\n+chr1\t4652666\t4652702\tregion_9923\t0\t+\n+chr1\t4652701\t4652737\tregion_9924\t0\t-\n+chr1\t4653073\t4653109\tregion_9925\t0\t-\n+chr1\t4653175\t4653211\tregion_9926\t0\t-\n+chr1\t4653188\t4653224\tregion_9927\t0\t+\n+chr1\t4653199\t4653235\tregion_9928\t0\t-\n+chr1\t4653277\t4653313\tregion_9929\t0\t+\n+chr1\t4653345\t4653381\tregion_9930\t0\t+\n+chr1\t4653387\t4653423\tregion_9931\t0\t-\n+chr1\t4653471\t4653507\tregion_9932\t0\t-\n+chr1\t4653503\t4653539\tregion_9933\t0\t-\n+chr1\t4653574\t4653610\tregion_9934\t0\t-\n+chr1\t4653665\t4653701\tregion_9935\t0\t+\n+chr1\t4655248\t4655284\tregion_9936\t0\t+\n+chr1\t4655485\t4655521\tregion_9937\t0\t+\n+chr1\t4656708\t4656744\tregion_9938\t0\t-\n+chr1\t4656721\t4656757\tregion_9939\t0\t-\n+chr1\t4656752\t4656788\tregion_9940\t0\t+\n+chr1\t4656810\t4656846\tregion_9941\t0\t-\n+chr1\t4657008\t4657044\tregion_9942\t0\t-\n+chr1\t4657224\t4657260\tregion_9943\t0\t-\n+chr1\t4657264\t4657300\tregion_9944\t0\t+\n+chr1\t4657354\t4657390\tregion_9945\t0\t+\n+chr1\t4657366\t4657402\tregion_9946\t0\t+\n+chr1\t4657389\t4657425\tregion_9947\t0\t+\n+chr1\t4657454\t4657490\tregion_9948\t0\t+\n+chr1\t4657590\t4657626\tregion_9949\t0\t-\n+chr1\t4657717\t4657753\tregion_9950\t0\t-\n+chr1\t4657724\t4657760\tregion_9951\t0\t-\n+chr1\t4657774\t4657810\tregion_9952\t0\t+\n+chr1\t4657836\t4657872\tregion_9953\t0\t-\n+chr1\t4657909\t4657945\tregion_9954\t0\t-\n+chr1\t4657912\t4657948\tregion_9955\t0\t+\n+chr1\t4657928\t4657964\tregion_9956\t0\t-\n+chr1\t4657951\t4657987\tregion_9957\t0\t+\n+chr1\t4658311\t4658347\tregion_9958\t0\t-\n+chr1\t4658321\t4658357\tregion_9959\t0\t+\n+chr1\t4658371\t4658407\tregion_9960\t0\t+\n+chr1\t4658397\t4658433\tregion_9961\t0\t+\n+chr1\t4658487\t4658523\tregion_9962\t0\t+\n+chr1\t4658664\t4658700\tregion_9963\t0\t-\n+chr1\t4658713\t4658749\tregion_9964\t0\t-\n+chr1\t4658824\t4658860\tregion_9965\t0\t-\n+chr1\t4658866\t4658902\tregion_9966\t0\t-\n+chr1\t4658905\t4658941\tregion_9967\t0\t+\n+chr1\t4658955\t4658991\tregion_9968\t0\t+\n+chr1\t4658971\t4659007\tregion_9969\t0\t-\n+chr1\t4659035\t4659071\tregion_9970\t0\t-\n+chr1\t4659244\t4659280\tregion_9971\t0\t-\n+chr1\t4659387\t4659423\tregion_9972\t0\t+\n+chr1\t4659465\t4659501\tregion_9973\t0\t-\n+chr1\t4659470\t4659506\tregion_9974\t0\t-\n+chr1\t4659504\t4659540\tregion_9975\t0\t-\n+chr1\t4659504\t4659540\tregion_9976\t0\t-\n+chr1\t4659511\t4659547\tregion_9977\t0\t-\n+chr1\t4659523\t4659559\tregion_9978\t0\t+\n+chr1\t4659530\t4659566\tregion_9979\t0\t-\n+chr1\t4659563\t4659599\tregion_9980\t0\t-\n+chr1\t4659578\t4659614\tregion_9981\t0\t-\n+chr1\t4659619\t4659655\tregion_9982\t0\t+\n+chr1\t4659698\t4659734\tregion_9983\t0\t+\n+chr1\t4659803\t4659839\tregion_9984\t0\t+\n+chr1\t4659846\t4659882\tregion_9985\t0\t+\n+chr1\t4659880\t4659916\tregion_9986\t0\t-\n+chr1\t4660125\t4660161\tregion_9987\t0\t-\n+chr1\t4660236\t4660272\tregion_9988\t0\t+\n+chr1\t4660334\t4660370\tregion_9989\t0\t+\n+chr1\t4660404\t4660440\tregion_9990\t0\t+\n+chr1\t4660431\t4660467\tregion_9991\t0\t-\n+chr1\t4661109\t4661145\tregion_9992\t0\t+\n+chr1\t4661186\t4661222\tregion_9993\t0\t+\n+chr1\t4661332\t4661368\tregion_9994\t0\t+\n+chr1\t4661506\t4661542\tregion_9995\t0\t+\n+chr1\t4661557\t4661593\tregion_9996\t0\t-\n+chr1\t4661619\t4661655\tregion_9997\t0\t-\n+chr1\t4662104\t4662140\tregion_9998\t0\t-\n+chr1\t4662148\t4662184\tregion_9999\t0\t+\n'

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/chipseq_input.bed.gz

Binary file test-data/chipseq_input.bed.gz has changed

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/config_TF.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/config_TF.txt Fri Dec 03 16:27:57 2021 +0000

@@ -0,0 +1,9 @@
+fragmentSize 200
+slidingWinSize 300
+movingStep 10
+isStrandSensitiveMode 1
+minCount 3
+outputNum 100000
+randomSeed 123456
+minScore 5.0
+bootstrapPass 50

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/genome_length_mm8_chr19.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_length_mm8_chr19.txt Fri Dec 03 16:27:57 2021 +0000

@@ -0,0 +1,1 @@
+chr19 61321190
\ No newline at end of file

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/hg18.len
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hg18.len Fri Dec 03 16:27:57 2021 +0000

@@ -0,0 +1,49 @@
+1 chr1 247249719
+2 chr2 242951149
+3 chr3 199501827
+4 chr4 191273063
+5 chr5 180857866
+6 chr6 170899992
+7 chr7 158821424
+8 chr8 146274826
+9 chr9 140273252
+10 chr10 135374737
+11 chr11 134452384
+12 chr12 132349534
+13 chr13 114142980
+14 chr14 106368585
+15 chr15 100338915
+16 chr16 88827254
+17 chr17 78774742
+18 chr18 76117153
+19 chr19 63811651
+20 chr20 62435964
+21 chr21 46944323
+22 chr22 49691432
+23 chrX 154913754
+24 chrY 57772954
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt
--- a/test-data/peakcalling_ccat/3.0/ccat_test_log_out_1.txt Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,131 +0,0 @@
-chromosome length information read. chromNum = 49!
-config file read.
-fragmentSize = 200
-isStrandSensitiveMode = 0
-slidingWinSize = 500
-movingStep = 50
-outputNum = 100000
-minCount = 4
-minScore = 5.000000
-bootstrapPass = 50
-randSeed = 123456
-reading tag files......
-10000 tags in L1, 10000 tags in L2.
-tag file read.
-pre-processing......
-pre-processing finished.
-estimating noise rate......
-not enough reads for noise rate estimation.
-noise rate estimation failed. noise rate set to be 1.0
-noise rate = 1.000000
-peak-finding......
-chr1......884 candidate peaks.
-chr1_random......0 candidate peaks.
-chr10......0 candidate peaks.
-chr10_random......0 candidate peaks.
-chr11......0 candidate peaks.
-chr11_random......0 candidate peaks.
-chr12......0 candidate peaks.
-chr13......0 candidate peaks.
-chr13_random......0 candidate peaks.
-chr14......0 candidate peaks.
-chr15......0 candidate peaks.
-chr15_random......0 candidate peaks.
-chr16......0 candidate peaks.
-chr16_random......0 candidate peaks.
-chr17......0 candidate peaks.
-chr17_random......0 candidate peaks.
-chr18......0 candidate peaks.
-chr18_random......0 candidate peaks.
-chr19......0 candidate peaks.
-chr19_random......0 candidate peaks.
-chr2......0 candidate peaks.
-chr2_random......0 candidate peaks.
-chr20......0 candidate peaks.
-chr21......0 candidate peaks.
-chr21_random......0 candidate peaks.
-chr22......0 candidate peaks.
-chr22_random......0 candidate peaks.
-chr22_h2_hap1......0 candidate peaks.
-chr3......0 candidate peaks.
-chr3_random......0 candidate peaks.
-chr4......0 candidate peaks.
-chr4_random......0 candidate peaks.
-chr5......0 candidate peaks.
-chr5_random......0 candidate peaks.
-chr5_h2_hap1......0 candidate peaks.
-chr6......0 candidate peaks.
-chr6_random......0 candidate peaks.
-chr6_cox_hap1......0 candidate peaks.
-chr6_qbl_hap2......0 candidate peaks.
-chr7......0 candidate peaks.
-chr7_random......0 candidate peaks.
-chr8......0 candidate peaks.
-chr8_random......0 candidate peaks.
-chr9......0 candidate peaks.
-chr9_random......0 candidate peaks.
-chrM......0 candidate peaks.
-chrX......0 candidate peaks.
-chrX_random......0 candidate peaks.
-chrY......0 candidate peaks.
-peak-finding finished.
-Significance Analysis......
-estimating paramters......
-smoothing factor = 0.356298
-estimating local FDR.....
-FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files.
-post-processing......
-chr1......finished.
-chr1_random......finished.
-chr10......finished.
-chr10_random......finished.
-chr11......finished.
-chr11_random......finished.
-chr12......finished.
-chr13......finished.
-chr13_random......finished.
-chr14......finished.
-chr15......finished.
-chr15_random......finished.
-chr16......finished.
-chr16_random......finished.
-chr17......finished.
-chr17_random......finished.
-chr18......finished.
-chr18_random......finished.
-chr19......finished.
-chr19_random......finished.
-chr2......finished.
-chr2_random......finished.
-chr20......finished.
-chr21......finished.
-chr21_random......finished.
-chr22......finished.
-chr22_random......finished.
-chr22_h2_hap1......finished.
-chr3......finished.
-chr3_random......finished.
-chr4......finished.
-chr4_random......finished.
-chr5......finished.
-chr5_random......finished.
-chr5_h2_hap1......finished.
-chr6......finished.
-chr6_random......finished.
-chr6_cox_hap1......finished.
-chr6_qbl_hap2......finished.
-chr7......finished.
-chr7_random......finished.
-chr8......finished.
-chr8_random......finished.
-chr9......finished.
-chr9_random......finished.
-chrM......finished.
-chrX......finished.
-chrX_random......finished.
-chrY......finished.
-post-processing finished.
-Significance analysis finished.
-saving results.......
-results saved.
-CCAT process completed!

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt
--- a/test-data/peakcalling_ccat/3.0/ccat_test_log_out_2.txt Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,131 +0,0 @@
-chromosome length information read. chromNum = 49!
-config file read.
-fragmentSize = 200
-isStrandSensitiveMode = 0
-slidingWinSize = 1000
-movingStep = 50
-outputNum = 100000
-minCount = 4
-minScore = 5.000000
-bootstrapPass = 50
-randSeed = 123456
-reading tag files......
-10000 tags in L1, 10000 tags in L2.
-tag file read.
-pre-processing......
-pre-processing finished.
-estimating noise rate......
-not enough reads for noise rate estimation.
-noise rate estimation failed. noise rate set to be 1.0
-noise rate = 1.000000
-peak-finding......
-chr1......673 candidate peaks.
-chr1_random......0 candidate peaks.
-chr10......0 candidate peaks.
-chr10_random......0 candidate peaks.
-chr11......0 candidate peaks.
-chr11_random......0 candidate peaks.
-chr12......0 candidate peaks.
-chr13......0 candidate peaks.
-chr13_random......0 candidate peaks.
-chr14......0 candidate peaks.
-chr15......0 candidate peaks.
-chr15_random......0 candidate peaks.
-chr16......0 candidate peaks.
-chr16_random......0 candidate peaks.
-chr17......0 candidate peaks.
-chr17_random......0 candidate peaks.
-chr18......0 candidate peaks.
-chr18_random......0 candidate peaks.
-chr19......0 candidate peaks.
-chr19_random......0 candidate peaks.
-chr2......0 candidate peaks.
-chr2_random......0 candidate peaks.
-chr20......0 candidate peaks.
-chr21......0 candidate peaks.
-chr21_random......0 candidate peaks.
-chr22......0 candidate peaks.
-chr22_random......0 candidate peaks.
-chr22_h2_hap1......0 candidate peaks.
-chr3......0 candidate peaks.
-chr3_random......0 candidate peaks.
-chr4......0 candidate peaks.
-chr4_random......0 candidate peaks.
-chr5......0 candidate peaks.
-chr5_random......0 candidate peaks.
-chr5_h2_hap1......0 candidate peaks.
-chr6......0 candidate peaks.
-chr6_random......0 candidate peaks.
-chr6_cox_hap1......0 candidate peaks.
-chr6_qbl_hap2......0 candidate peaks.
-chr7......0 candidate peaks.
-chr7_random......0 candidate peaks.
-chr8......0 candidate peaks.
-chr8_random......0 candidate peaks.
-chr9......0 candidate peaks.
-chr9_random......0 candidate peaks.
-chrM......0 candidate peaks.
-chrX......0 candidate peaks.
-chrX_random......0 candidate peaks.
-chrY......0 candidate peaks.
-peak-finding finished.
-Significance Analysis......
-estimating paramters......
-smoothing factor = 0.287387
-estimating local FDR.....
-FDR at the threshold 5.000000 is 0.999000. You may want to adjust the threshold by inspecting the output files.
-post-processing......
-chr1......finished.
-chr1_random......finished.
-chr10......finished.
-chr10_random......finished.
-chr11......finished.
-chr11_random......finished.
-chr12......finished.
-chr13......finished.
-chr13_random......finished.
-chr14......finished.
-chr15......finished.
-chr15_random......finished.
-chr16......finished.
-chr16_random......finished.
-chr17......finished.
-chr17_random......finished.
-chr18......finished.
-chr18_random......finished.
-chr19......finished.
-chr19_random......finished.
-chr2......finished.
-chr2_random......finished.
-chr20......finished.
-chr21......finished.
-chr21_random......finished.
-chr22......finished.
-chr22_random......finished.
-chr22_h2_hap1......finished.
-chr3......finished.
-chr3_random......finished.
-chr4......finished.
-chr4_random......finished.
-chr5......finished.
-chr5_random......finished.
-chr5_h2_hap1......finished.
-chr6......finished.
-chr6_random......finished.
-chr6_cox_hap1......finished.
-chr6_qbl_hap2......finished.
-chr7......finished.
-chr7_random......finished.
-chr8......finished.
-chr8_random......finished.
-chr9......finished.
-chr9_random......finished.
-chrM......finished.
-chrX......finished.
-chrX_random......finished.
-chrY......finished.
-post-processing finished.
-Significance analysis finished.
-saving results.......
-results saved.
-CCAT process completed!

diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match
--- a/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match
--- a/test-data/peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,272 +0,0 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diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match
--- a/test-data/peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,183 +0,0 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diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match
--- a/test-data/peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,74 +0,0 @@
-chr1 4760225 4725450 4779800 139 0 507\.\d+ 0\.025000
-chr1 5061725 5053400 5068550 19 0 69\.\d+ 0\.025000
-chr1 5094825 5080750 5101500 19 0 69\.\d+ 0\.025000
-chr1 5174775 5163300 5181450 19 0 69\.\d+ 0\.025000
-chr1 5198075 5193000 5227900 17 0 62\.\d+ 0\.025000
-chr1 5593825 5575300 5618600 17 0 62\.\d+ 0\.025000
-chr1 4716275 4707550 4722700 16 0 58\.\d+ 0\.025000
-chr1 4961575 4951600 4964800 15 0 54\.\d+ 0\.025000
-chr1 4996075 4990250 5026600 15 0 54\.\d+ 0\.025000
-chr1 4792775 4788500 4798400 14 0 51\.\d+ 0\.025000
-chr1 4820975 4818750 4863650 14 0 51\.\d+ 0\.025000
-chr1 4892125 4888750 4938450 14 0 51\.\d+ 0\.025000
-chr1 4811575 4798500 4818650 14 0 51\.\d+ 0\.025000
-chr1 5132075 5121600 5140300 14 0 51\.\d+ 0\.025000
-chr1 5078525 5073200 5080700 13 0 47\.\d+ 0\.025000
-chr1 5249925 5247000 5258700 13 0 47\.\d+ 0\.025000
-chr1 4666375 4662050 4671350 13 0 47\.\d+ 0\.025000
-chr1 5649475 5645550 5668850 13 0 47\.\d+ 0\.025000
-chr1 4872625 4871150 4888250 12 0 43\.\d+ 0\.025000
-chr1 5510825 5501200 5517200 12 0 43\.\d+ 0\.025000
-chr1 4967025 4965050 4970850 12 0 43\.\d+ 0\.025000
-chr1 5306825 5300700 5319250 12 0 43\.\d+ 0\.025000
-chr1 5270275 5269300 5281550 11 0 40\.\d+ 0\.034000
-chr1 5570325 5567450 5573850 11 0 40\.\d+ 0\.034000
-chr1 5106525 5105050 5117450 11 0 40\.\d+ 0\.034000
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-chr1 5364775 5357550 5366350 8 0 29\.\d+ 0\.034000
-chr1 5401025 5390850 5406350 8 0 29\.\d+ 0\.034000
-chr1 5324575 5322550 5334750 8 0 29\.\d+ 0\.034000
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-chr1 5716025 5711700 5719950 7 0 25\.\d+ 0\.135000
-chr1 5496625 5495200 5499750 7 0 25\.\d+ 0\.135000
-chr1 5695175 5693900 5701400 7 0 25\.\d+ 0\.135000
-chr1 4787225 4783350 4788300 7 0 25\.\d+ 0\.135000
-chr1 5751925 5749150 5753500 7 0 25\.\d+ 0\.135000
-chr1 5453625 5450900 5458700 7 0 25\.\d+ 0\.135000
-chr1 5688775 5687300 5691900 6 0 21\.\d+ 0\.135000
-chr1 5632975 5631350 5638100 6 0 21\.\d+ 0\.135000
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-chr1 5487825 5482700 5489150 6 0 21\.\d+ 0\.135000
-chr1 5539925 5538950 5542250 6 0 21\.\d+ 0\.135000
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-chr1 4507925 4507250 4509100 44 2 20\.\d+ 0\.199000
-chr1 5161725 5159000 5163250 5 0 18\.\d+ 0\.199000
-chr1 4781325 4780250 4782350 5 0 18\.\d+ 0\.199000
-chr1 5475625 5474600 5479600 5 0 18\.\d+ 0\.199000
-chr1 5039275 5037850 5040800 5 0 18\.\d+ 0\.199000
-chr1 4337875 4336700 4338600 60 4 14\.\d+ 0\.199000
-chr1 3023575 3022750 3024750 4 0 14\.\d+ 1\.000000
-chr1 5033175 5032000 5036100 4 0 14\.\d+ 1\.000000
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-chr1 4408525 4407200 4409200 88 13 6\.\d+ 1\.000000
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diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match
--- a/test-data/peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r 201d8e7dfc43 -r 1a6979fbd544 test-data/peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match
--- a/test-data/peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,673 +0,0 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diff -r 201d8e7dfc43 -r 1a6979fbd544 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Dec 03 16:27:57 2021 +0000

@@ -0,0 +1,8 @@
+
+<tables>
+    
+    <table name="ccat_configurations" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/ccat_configurations.loc" />
+    </table>
+</tables>

diff -r 201d8e7dfc43 -r 1a6979fbd544 tool_dependencies.xml
--- a/tool_dependencies.xml Tue Jul 21 14:13:34 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="CCAT" version="3.0">
-      <repository changeset_revision="b65b1bab9226" name="package_ccat_3_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>