# HG changeset patch
# User fubar
# Date 1377758828 14400
# Node ID 08cb01b2b9d7a3b2c968687bd88f47e776d50a7b
# Parent  640b1432caa416003ebfacdb84d392bbc012f8ec
Uploaded

diff -r 640b1432caa4 -r 08cb01b2b9d7 rlGAT/test-data/GATcontigs.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rlGAT/test-data/GATcontigs.bed	Thu Aug 29 02:47:08 2013 -0400
@@ -0,0 +1,25 @@
+chr13	0	115169878	ws
+chr12	0	133851895	ws
+chr11	0	135006516	ws
+chr10	0	135534747	ws
+chr17	0	81195210	ws
+chr16	0	90354753	ws
+chr15	0	102531392	ws
+chr14	0	107349540	ws
+chr19	0	59128983	ws
+chr18	0	78077248	ws
+chr3	0	198022430	ws
+chr2	0	243199373	ws
+chrY	0	59373566	ws
+chrX	0	155270560	ws
+chrM	0	16571	ws
+chr22	0	51304566	ws
+chr20	0	63025520	ws
+chr21	0	48129895	ws
+chr7	0	159138663	ws
+chr6	0	171115067	ws
+chr5	0	180915260	ws
+chr4	0	191154276	ws
+chr1	0	249250621	ws
+chr9	0	141213431	ws
+chr8	0	146364022	ws
diff -r 640b1432caa4 -r 08cb01b2b9d7 rlGAT/test-data/GATjurkat.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rlGAT/test-data/GATjurkat.bed	Thu Aug 29 02:47:08 2013 -0400
@@ -0,0 +1,159614 @@
+track name="tb_wgEncodeUwDnaseJurkatPkRep1" description="table browser query on wgEncodeUwDnaseJurkatPkRep1" visibility=3 url= 
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diff -r 640b1432caa4 -r 08cb01b2b9d7 rlGAT/test-data/GATsrf.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rlGAT/test-data/GATsrf.bed	Thu Aug 29 02:47:08 2013 -0400
@@ -0,0 +1,556 @@
+chr5	60627981	60628031	SRF.1
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diff -r 640b1432caa4 -r 08cb01b2b9d7 rlGAT/test-data/gat_test1_out.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rlGAT/test-data/gat_test1_out.log	Thu Aug 29 02:47:08 2013 -0400
@@ -0,0 +1,82 @@
+# output generated by /mnt/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/fubar/genomic_association_tester/640b1432caa4/genomic_association_tester/rlGAT/gat-run.py --ignore-segment-tracks --log=/mnt/galaxy/tmp/job_working_directory/000/102/galaxy_dataset_195.dat --num-samples=1000 --segment-file /mnt/galaxy/files/000/dataset_185.dat --workspace-file /mnt/galaxy/files/000/dataset_186.dat --annotation-file /mnt/galaxy/files/000/dataset_188.dat
+# job started at Thu Aug 29 05:50:37 2013 on server-d96376c2-cd09-4b9c-af66-3046d5eba53e -- 56ea3024-f0c4-4f44-964c-2fec5b8d363e
+# pid: 18342, system: Linux 3.2.0-49-virtual #75-Ubuntu SMP Tue Jun 18 17:59:38 UTC 2013 x86_64
+# annotation_files                        : [\'/mnt/galaxy/files/000/dataset_188.dat\']
+# bucket_size                             : 1
+# cache                                   : None
+# conditional                             : unconditional
+# conditional_expansion                   : None
+# conditional_extension                   : None
+# counters                                : []
+# enable_split_tracks                     : False
+# ignore_segment_tracks                   : True
+# input_filename_counts                   : None
+# input_filename_descriptions             : None
+# input_filename_results                  : None
+# isochore_files                          : None
+# loglevel                                : 1
+# nbuckets                                : 100000
+# null                                    : default
+# num_samples                             : 1000
+# num_threads                             : 0
+# output_bed                              : []
+# output_counts_pattern                   : None
+# output_filename_pattern                 : %s
+# output_force                            : False
+# output_order                            : fold
+# output_plots_pattern                    : None
+# output_samples_pattern                  : None
+# output_stats                            : []
+# output_tables_pattern                   : %s.tsv.gz
+# pseudo_count                            : 1.0
+# pvalue_method                           : empirical
+# qvalue_lambda                           : None
+# qvalue_method                           : BH
+# qvalue_pi0_method                       : smoother
+# restrict_workspace                      : False
+# sample_files                            : []
+# sampler                                 : annotator
+# segment_files                           : [\'/mnt/galaxy/files/000/dataset_185.dat\']
+# shift_expansion                         : 2.0
+# shift_extension                         : 0
+# stderr                                  : <open file \'<stderr>\', mode \'w\' at 0x2b40e39fa270>
+# stdin                                   : <open file \'<stdin>\', mode \'r\' at 0x2b40e39fa150>
+# stdlog                                  : <open file \'/mnt/galaxy/tmp/job_working_directory/000/102/galaxy_dataset_195.dat\', mode \'a\' at 0x2aaed20>
+# stdout                                  : <open file \'<stdout>\', mode \'w\' at 0x2b40e39fa1e0>
+# timeit_file                             : None
+# timeit_header                           : None
+# timeit_name                             : all
+# truncate_segments_to_workspace          : False
+# truncate_workspace_to_annotations       : False
+# workspace_files                         : [\'/mnt/galaxy/files/000/dataset_186.dat\']
+2013-08-29 05:50:37,596 INFO segments: reading tracks from 1 files
+2013-08-29 05:50:37,604 INFO segments: read 556 tracks from 1 files
+2013-08-29 05:50:37,606 INFO merged all segments into one track with 1 segments
+2013-08-29 05:50:37,606 INFO annotations: reading tracks from 1 files
+2013-08-29 05:50:38,254 INFO annotations: read 1 tracks from 1 files
+2013-08-29 05:50:38,264 INFO workspaces: reading tracks from 1 files
+2013-08-29 05:50:38,264 INFO workspaces: read 1 tracks from 1 files
+2013-08-29 05:50:38,264 INFO collapsing workspaces
+2013-08-29 05:50:38,264 INFO intervals loaded in 0 seconds
+2013-08-29 05:50:38,266 INFO collecting observed counts
+2013-08-29 05:50:38,267 INFO starting sampling
+2013-08-29 05:50:38,267 INFO sampling: merged: 1/1
+2013-08-29 05:50:38,267 INFO performing unconditional sampling
+2013-08-29 05:50:38,268 INFO workspace without conditioning: 25 segments, 3095693983 nucleotides
+2013-08-29 05:50:38,268 INFO workspace after conditioning: 25 segments, 3095693983 nucleotides
+2013-08-29 05:50:38,270 INFO sampling started
+2013-08-29 05:50:38,291 INFO 0/1000 done ( 0.00)
+2013-08-29 05:50:40,016 INFO 100/1000 done (10.00)
+2013-08-29 05:50:41,747 INFO 200/1000 done (20.00)
+2013-08-29 05:50:43,486 INFO 300/1000 done (30.00)
+2013-08-29 05:50:45,207 INFO 400/1000 done (40.00)
+2013-08-29 05:50:46,960 INFO 500/1000 done (50.00)
+2013-08-29 05:50:48,733 INFO 600/1000 done (60.00)
+2013-08-29 05:50:50,451 INFO 700/1000 done (70.00)
+2013-08-29 05:50:52,175 INFO 800/1000 done (80.00)
+2013-08-29 05:50:53,884 INFO 900/1000 done (90.00)
+2013-08-29 05:50:55,583 INFO sampling completed
+2013-08-29 05:50:55,586 INFO sampling finished: 
+2013-08-29 05:50:55,586 INFO computing PValue statistics
+2013-08-29 05:50:55,589 INFO computing FDR statistics
+# job finished in 17 seconds at Thu Aug 29 05:50:55 2013 -- 19.27  0.17  0.01  0.01 -- 56ea3024-f0c4-4f44-964c-2fec5b8d363e
diff -r 640b1432caa4 -r 08cb01b2b9d7 rlGAT/test-data/gat_test1_out.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rlGAT/test-data/gat_test1_out.tsv	Thu Aug 29 02:47:08 2013 -0400
@@ -0,0 +1,2 @@
+track	annotation	observed	expected	CI95low	CI95high	stddev	fold	l2fold	pvalue	qvalue	track_nsegments	track_size	track_density	annotation_nsegments	annotation_size	annotation_density	overlap_nsegments	overlap_size	overlap_density	percent_overlap_nsegments_track	percent_overlap_size_track	percent_overlap_nsegments_annotation	percent_overlap_size_annotation
+merged	tb_wgEncodeUwDnaseJurkatPkRep1	20183	250.9830	91.0000	439.0000	105.1195	80.1006	6.3237	1.0000e-03	1.0000e-03	556	27800	8.9802e-04	159613	23959670	7.7397e-01	450	20183	6.5197e-04	80.9353	72.6007	0.2819	0.0842