Mercurial > repos > greg > repmatch_gff3
changeset 12:34d134cd4ca9 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 16 Dec 2015 14:45:32 -0500 |
| parents | 91e663440ca4 |
| children | d31ef9abce74 |
| files | repmatch_gff3.xml static/images/._repmatch.png static/images/repmatch.png test-data/closest_matched_pairs_input1.gff test-data/closest_s_input1.gff test-data/histogram_out1.pdf test-data/key_out1.tabular test-data/largest_matched_pairs_input1.gff test-data/largest_s_input1.gff test-data/matched_peaks_out1.gff test-data/orphan_out1.tabular test-data/statistics_histogram_out1.pdf test-data/statistics_table_out1.tabular test-data/summary_out1.gff test-data/unmatched_peaks_out1.tabular tool_dependencies.xml |
| diffstat | 16 files changed, 227 insertions(+), 210 deletions(-) [+] |
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--- a/repmatch_gff3.xml Wed Dec 02 20:32:21 2015 -0500 +++ b/repmatch_gff3.xml Wed Dec 16 14:45:32 2015 -0500 @@ -95,20 +95,37 @@ <help> **What it does** -Replicate matching - inspects paired peaks from two or more replicates and produces a list of matched -paired peaks and optionally a list of unmatched paired peaks. Additional optional outputs include the -median read count for each input, details and a histogram. +RepMatch accepts two or more input datasets, and starts by defining peak-pair midpoints in the first dataset. It then +discovers all peak-pair midpoints in the second dataset that are within the distance, defined by the tool's **Maximum +distance between peaks in different replicates to allow merging** parameter, from the peak-pair midpoint coordinate in +the first dataset. When encountering multiple candidates to match (one-to-many), RepMatch uses the method defined by +the tool's **Method of finding match** parameter so that there is at most only a one-to-one match across the two datasets. +This method provides the following options: + + * **closest** - matches only the closest one in bp distance. + * **largest** - matches the one that contain the most number of reads. + * **all** - both methods are run separately. + +RepMatch matching is an iterative process, as it attempts to find the centroid coordinate amongst all replicates. As such, +the centroid is the point of reference for "distqnce" and "closest". This process can be sped up by increasing the tool's +**Step size** parameter. + +The minimum number of replicates that can be matched for a match to occur is defined by the tool's **Minimum number of +replicates that must be matched for merging to occur** parameter. Additional filters can be applied using the tool's +**Advanced options**, including a lower and upper limit for the C-W distance. + +.. image:: $PATH_TO_IMAGES/repmatch.png ----- **Options** -* **Distance** - Maximum distance between peaks in different replicates to allow merging. -* **Method** - Method to use when calling replicates. -* **Step Size** - Distance for each iteration. -* **Replicates** - Minimum number of replicates to call a peak. Number of replicates required must be at least 2. -* **Lower Limit** - Lower limit for the Crick-Watson distance filter. -* **Upper Limit** - Upper limit for the Crick-Watson distance filter. + * **Distance** - Maximum distance for discovering all peak-pair midpoints in a second dataset relative to the peak-pair midpoints in the first dataset + * **Method** - Method to use when encountering multiple candidates to match so that there is at most only a one-to-one match across the two datasets. + * **Step Size** - Distance for each iteration. + * **Replicates** - Minimum number of replicates that can be matched for a match to occur. This value must be at least 2. + * **Lower Limit** - Lower limit for the Crick-Watson distance filter. + * **Upper Limit** - Upper limit for the Crick-Watson distance filter. </help> <expand macro="citations" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/closest_matched_pairs_input1.gff Wed Dec 16 14:45:32 2015 -0500 @@ -0,0 +1,66 @@ +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14 +chr1 cwpair . 265 266 2474.0 . . cw_distance=48 +chr1 cwpair . 268 269 4088.0 . . cw_distance=6 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16 +chr1 cwpair . 370 371 899.0 . . cw_distance=25 +chr1 cwpair . 388 389 359.0 . . cw_distance=20 +chr1 cwpair . 452 453 504.0 . . cw_distance=8 +chr1 cwpair . 500 501 569.0 . . cw_distance=-44 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 +chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 +chr1 cwpair . 230178 230179 56.0 . . cw_distance=10
--- a/test-data/closest_s_input1.gff Wed Dec 02 20:32:21 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 218 219 4022.0 . . cw_distance=14 -chr1 cwpair . 265 266 2474.0 . . cw_distance=48 -chr1 cwpair . 268 269 4088.0 . . cw_distance=6 -chr1 cwpair . 325 326 1171.0 . . cw_distance=16 -chr1 cwpair . 370 371 899.0 . . cw_distance=25 -chr1 cwpair . 388 389 359.0 . . cw_distance=20 -chr1 cwpair . 452 453 504.0 . . cw_distance=8 -chr1 cwpair . 500 501 569.0 . . cw_distance=-44 -chr1 cwpair . 668 669 319.0 . . cw_distance=-48 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 -chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11 -chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 92567 92568 789.0 . . cw_distance=28 -chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 -chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 -chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 -chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 230125 230126 44.0 . . cw_distance=10 -chr1 cwpair . 230157 230158 15.0 . . cw_distance=5 -chr1 cwpair . 230178 230179 56.0 . . cw_distance=10
--- a/test-data/key_out1.tabular Wed Dec 02 20:32:21 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -data median read count -1 783.5 -2 790.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/largest_matched_pairs_input1.gff Wed Dec 16 14:45:32 2015 -0500 @@ -0,0 +1,64 @@ +chr1 cwpair . 59 60 2881.0 . . cw_distance=2 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59 +chr1 cwpair . 245 246 5421.0 . . cw_distance=-40 +chr1 cwpair . 250 251 2739.0 . . cw_distance=78 +chr1 cwpair . 256 257 2424.0 . . cw_distance=30 +chr1 cwpair . 345 346 1185.0 . . cw_distance=-25 +chr1 cwpair . 350 351 885.0 . . cw_distance=66 +chr1 cwpair . 417 418 362.0 . . cw_distance=78 +chr1 cwpair . 463 464 802.0 . . cw_distance=30 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 +chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 +chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 +chr1 cwpair . 87015 87016 834.0 . . cw_distance=-28 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 +chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 +chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 +chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 +chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 +chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 +chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 +chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 +chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- a/test-data/largest_s_input1.gff Wed Dec 02 20:32:21 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 245 246 5421.0 . . cw_distance=-40 -chr1 cwpair . 250 251 2739.0 . . cw_distance=78 -chr1 cwpair . 256 257 2424.0 . . cw_distance=30 -chr1 cwpair . 345 346 1185.0 . . cw_distance=-25 -chr1 cwpair . 350 351 885.0 . . cw_distance=66 -chr1 cwpair . 417 418 362.0 . . cw_distance=78 -chr1 cwpair . 463 464 802.0 . . cw_distance=30 -chr1 cwpair . 668 669 319.0 . . cw_distance=-48 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 72786 72787 1063.0 . . cw_distance=-10 -chr1 cwpair . 87011 87012 2370.0 . . cw_distance=95 -chr1 cwpair . 87015 87016 834.0 . . cw_distance=-28 -chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3 -chr1 cwpair . 87174 87175 3475.0 . . cw_distance=-13 -chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 -chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 -chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 197535 197536 5.0 . . cw_distance=73 -chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 -chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16 -chr1 cwpair . 229762 229763 699.0 . . cw_distance=63 -chr1 cwpair . 230142 230143 10.0 . . cw_distance=-25 -chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 -chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/matched_peaks_out1.gff Wed Dec 16 14:45:32 2015 -0500 @@ -0,0 +1,64 @@ +chr1 repmatch . 87168 87169 4488.704113924051 . . median_distance=-1;value_sum=9006.0;replicates=2 +chr1 repmatch . 229759 229760 4512.3598101265825 . . median_distance=16;value_sum=9062.0;replicates=2 +chr1 repmatch . 123 124 4186.70506329114 . . median_distance=52;value_sum=8408.0;replicates=2 +chr1 repmatch . 262 263 3246.0278481012656 . . median_distance=18;value_sum=6512.0;replicates=2 +chr1 repmatch . 231 232 4699.198417721519 . . median_distance=-13;value_sum=9443.0;replicates=2 +chr1 repmatch . 87188 87189 4647.554746835443 . . median_distance=39;value_sum=9342.0;replicates=2 +chr1 repmatch . 59 60 2869.1477848101267 . . median_distance=2;value_sum=5762.0;replicates=2 +chr1 repmatch . 257 258 2595.2319620253165 . . median_distance=63;value_sum=5213.0;replicates=2 +chr1 repmatch . 92651 92652 1420.1610759493672 . . median_distance=20;value_sum=2844.0;replicates=2 +chr1 repmatch . 101399 101400 2351.2870253164556 . . median_distance=-44;value_sum=4722.0;replicates=2 +chr1 repmatch . 87109 87110 2249.7066455696204 . . median_distance=3;value_sum=4518.0;replicates=2 +chr1 repmatch . 156 157 2168.043987341772 . . median_distance=59;value_sum=4354.0;replicates=2 +chr1 repmatch . 70792 70793 2137.171518987342 . . median_distance=12;value_sum=4292.0;replicates=2 +chr1 repmatch . 6218 6219 2116.257911392405 . . median_distance=91;value_sum=4250.0;replicates=2 +chr1 repmatch . 86996 86997 2181.75 . . median_distance=66;value_sum=4383.0;replicates=2 +chr1 repmatch . 169095 169096 1879.2370253164559 . . median_distance=-43;value_sum=3774.0;replicates=2 +chr1 repmatch . 155079 155080 1566.5287974683545 . . median_distance=83;value_sum=3146.0;replicates=2 +chr1 repmatch . 203863 203864 1469.9278481012657 . . median_distance=-37;value_sum=2952.0;replicates=2 +chr1 repmatch . 92421 92422 1382.2898734177215 . . median_distance=0;value_sum=2776.0;replicates=2 +chr1 repmatch . 185109 185110 1365.3598101265823 . . median_distance=46;value_sum=2742.0;replicates=2 +chr1 repmatch . 39076 39077 1344.4462025316457 . . median_distance=-29;value_sum=2700.0;replicates=2 +chr1 repmatch . 6454 6455 1243.8617088607593 . . median_distance=63;value_sum=2498.0;replicates=2 +chr1 repmatch . 87029 87030 1009.0689873417721 . . median_distance=1;value_sum=2025.0;replicates=2 +chr1 repmatch . 25305 25306 1178.1332278481013 . . median_distance=99;value_sum=2366.0;replicates=2 +chr1 repmatch . 139230 139231 1174.1496835443038 . . median_distance=15;value_sum=2358.0;replicates=2 +chr1 repmatch . 335 336 1173.125 . . median_distance=-5;value_sum=2356.0;replicates=2 +chr1 repmatch . 55548 55549 952.067088607595 . . median_distance=86;value_sum=1912.0;replicates=2 +chr1 repmatch . 360 361 888.3591772151899 . . median_distance=45;value_sum=1784.0;replicates=2 +chr1 repmatch . 72795 72796 961.6268987341772 . . median_distance=9;value_sum=1932.0;replicates=2 +chr1 repmatch . 22580 22581 859.4496835443038 . . median_distance=-2;value_sum=1726.0;replicates=2 +chr1 repmatch . 199413 199414 806.6677215189873 . . median_distance=-30;value_sum=1620.0;replicates=2 +chr1 repmatch . 92584 92585 1800.832911392405 . . median_distance=62;value_sum=3625.0;replicates=2 +chr1 repmatch . 19213 19214 774.7993670886076 . . median_distance=-25;value_sum=1556.0;replicates=2 +chr1 repmatch . 116649 116650 769.8199367088607 . . median_distance=-41;value_sum=1546.0;replicates=2 +chr1 repmatch . 124306 124307 757.8693037974683 . . median_distance=-43;value_sum=1522.0;replicates=2 +chr1 repmatch . 113782 113783 713.0544303797469 . . median_distance=-20;value_sum=1432.0;replicates=2 +chr1 repmatch . 138876 138877 708.075 . . median_distance=-4;value_sum=1422.0;replicates=2 +chr1 repmatch . 229762 229763 696.1243670886076 . . median_distance=63;value_sum=1398.0;replicates=2 +chr1 repmatch . 95955 95956 686.1655063291139 . . median_distance=51;value_sum=1378.0;replicates=2 +chr1 repmatch . 134230 134231 656.2889240506329 . . median_distance=100;value_sum=1318.0;replicates=2 +chr1 repmatch . 170134 170135 654.2971518987342 . . median_distance=10;value_sum=1314.0;replicates=2 +chr1 repmatch . 228672 228673 623.4246835443038 . . median_distance=58;value_sum=1252.0;replicates=2 +chr1 repmatch . 65160 65161 615.4575949367088 . . median_distance=-4;value_sum=1236.0;replicates=2 +chr1 repmatch . 151365 151366 592.5522151898734 . . median_distance=-28;value_sum=1190.0;replicates=2 +chr1 repmatch . 108611 108612 570.6427215189874 . . median_distance=-45;value_sum=1146.0;replicates=2 +chr1 repmatch . 106047 106048 569.646835443038 . . median_distance=7;value_sum=1144.0;replicates=2 +chr1 repmatch . 481 482 682.2006329113924 . . median_distance=-7;value_sum=1371.0;replicates=2 +chr1 repmatch . 59228 59229 562.6756329113924 . . median_distance=56;value_sum=1130.0;replicates=2 +chr1 repmatch . 173276 173277 543.7537974683544 . . median_distance=8;value_sum=1092.0;replicates=2 +chr1 repmatch . 434 435 431.5107594936709 . . median_distance=43;value_sum=866.0;replicates=2 +chr1 repmatch . 45670 45671 490.971835443038 . . median_distance=-35;value_sum=986.0;replicates=2 +chr1 repmatch . 31670 31671 487.9841772151899 . . median_distance=66;value_sum=980.0;replicates=2 +chr1 repmatch . 32483 32484 476.0335443037975 . . median_distance=48;value_sum=956.0;replicates=2 +chr1 repmatch . 6714 6715 431.218670886076 . . median_distance=-4;value_sum=866.0;replicates=2 +chr1 repmatch . 136369 136370 363.498417721519 . . median_distance=-14;value_sum=730.0;replicates=2 +chr1 repmatch . 39237 39238 360.5107594936709 . . median_distance=61;value_sum=724.0;replicates=2 +chr1 repmatch . 668 669 317.6876582278481 . . median_distance=-48;value_sum=638.0;replicates=2 +chr1 repmatch . 98551 98552 121.49810126582278 . . median_distance=27;value_sum=244.0;replicates=2 +chr1 repmatch . 180331 180332 96.60094936708862 . . median_distance=82;value_sum=194.0;replicates=2 +chr1 repmatch . 230172 230173 42.87658227848101 . . median_distance=-2;value_sum=86.0;replicates=2 +chr1 repmatch . 230133 230134 26.95886075949367 . . median_distance=-8;value_sum=54.0;replicates=2 +chr1 repmatch . 230154 230155 44.69145569620253 . . median_distance=34;value_sum=90.0;replicates=2 +chr1 repmatch . 96919 96920 11.950632911392404 . . median_distance=3;value_sum=24.0;replicates=2 +chr1 repmatch . 197535 197536 4.9794303797468356 . . median_distance=73;value_sum=10.0;replicates=2
--- a/test-data/orphan_out1.tabular Wed Dec 02 20:32:21 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -chrom midpoint midpoint+1 c-w sum c-w distance replicate id -chr1 388 389 359.0 20 1 -chr1 72731 72732 710.0 100 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/statistics_table_out1.tabular Wed Dec 16 14:45:32 2015 -0500 @@ -0,0 +1,3 @@ +data median read count +1 783.5 +2 790.0
--- a/test-data/summary_out1.gff Wed Dec 02 20:32:21 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -chr1 repmatch . 87168 87169 4488.704113924051 . . median_distance=-1;value_sum=9006.0;replicates=2 -chr1 repmatch . 229759 229760 4512.3598101265825 . . median_distance=16;value_sum=9062.0;replicates=2 -chr1 repmatch . 123 124 4186.70506329114 . . median_distance=52;value_sum=8408.0;replicates=2 -chr1 repmatch . 262 263 3246.0278481012656 . . median_distance=18;value_sum=6512.0;replicates=2 -chr1 repmatch . 231 232 4699.198417721519 . . median_distance=-13;value_sum=9443.0;replicates=2 -chr1 repmatch . 87188 87189 4647.554746835443 . . median_distance=39;value_sum=9342.0;replicates=2 -chr1 repmatch . 59 60 2869.1477848101267 . . median_distance=2;value_sum=5762.0;replicates=2 -chr1 repmatch . 257 258 2595.2319620253165 . . median_distance=63;value_sum=5213.0;replicates=2 -chr1 repmatch . 92651 92652 1420.1610759493672 . . median_distance=20;value_sum=2844.0;replicates=2 -chr1 repmatch . 101399 101400 2351.2870253164556 . . median_distance=-44;value_sum=4722.0;replicates=2 -chr1 repmatch . 87109 87110 2249.7066455696204 . . median_distance=3;value_sum=4518.0;replicates=2 -chr1 repmatch . 156 157 2168.043987341772 . . median_distance=59;value_sum=4354.0;replicates=2 -chr1 repmatch . 70792 70793 2137.171518987342 . . median_distance=12;value_sum=4292.0;replicates=2 -chr1 repmatch . 6218 6219 2116.257911392405 . . median_distance=91;value_sum=4250.0;replicates=2 -chr1 repmatch . 86996 86997 2181.75 . . median_distance=66;value_sum=4383.0;replicates=2 -chr1 repmatch . 169095 169096 1879.2370253164559 . . median_distance=-43;value_sum=3774.0;replicates=2 -chr1 repmatch . 155079 155080 1566.5287974683545 . . median_distance=83;value_sum=3146.0;replicates=2 -chr1 repmatch . 203863 203864 1469.9278481012657 . . median_distance=-37;value_sum=2952.0;replicates=2 -chr1 repmatch . 92421 92422 1382.2898734177215 . . median_distance=0;value_sum=2776.0;replicates=2 -chr1 repmatch . 185109 185110 1365.3598101265823 . . median_distance=46;value_sum=2742.0;replicates=2 -chr1 repmatch . 39076 39077 1344.4462025316457 . . median_distance=-29;value_sum=2700.0;replicates=2 -chr1 repmatch . 6454 6455 1243.8617088607593 . . median_distance=63;value_sum=2498.0;replicates=2 -chr1 repmatch . 87029 87030 1009.0689873417721 . . median_distance=1;value_sum=2025.0;replicates=2 -chr1 repmatch . 25305 25306 1178.1332278481013 . . median_distance=99;value_sum=2366.0;replicates=2 -chr1 repmatch . 139230 139231 1174.1496835443038 . . median_distance=15;value_sum=2358.0;replicates=2 -chr1 repmatch . 335 336 1173.125 . . median_distance=-5;value_sum=2356.0;replicates=2 -chr1 repmatch . 55548 55549 952.067088607595 . . median_distance=86;value_sum=1912.0;replicates=2 -chr1 repmatch . 360 361 888.3591772151899 . . median_distance=45;value_sum=1784.0;replicates=2 -chr1 repmatch . 72795 72796 961.6268987341772 . . median_distance=9;value_sum=1932.0;replicates=2 -chr1 repmatch . 22580 22581 859.4496835443038 . . median_distance=-2;value_sum=1726.0;replicates=2 -chr1 repmatch . 199413 199414 806.6677215189873 . . median_distance=-30;value_sum=1620.0;replicates=2 -chr1 repmatch . 92584 92585 1800.832911392405 . . median_distance=62;value_sum=3625.0;replicates=2 -chr1 repmatch . 19213 19214 774.7993670886076 . . median_distance=-25;value_sum=1556.0;replicates=2 -chr1 repmatch . 116649 116650 769.8199367088607 . . median_distance=-41;value_sum=1546.0;replicates=2 -chr1 repmatch . 124306 124307 757.8693037974683 . . median_distance=-43;value_sum=1522.0;replicates=2 -chr1 repmatch . 113782 113783 713.0544303797469 . . median_distance=-20;value_sum=1432.0;replicates=2 -chr1 repmatch . 138876 138877 708.075 . . median_distance=-4;value_sum=1422.0;replicates=2 -chr1 repmatch . 229762 229763 696.1243670886076 . . median_distance=63;value_sum=1398.0;replicates=2 -chr1 repmatch . 95955 95956 686.1655063291139 . . median_distance=51;value_sum=1378.0;replicates=2 -chr1 repmatch . 134230 134231 656.2889240506329 . . median_distance=100;value_sum=1318.0;replicates=2 -chr1 repmatch . 170134 170135 654.2971518987342 . . median_distance=10;value_sum=1314.0;replicates=2 -chr1 repmatch . 228672 228673 623.4246835443038 . . median_distance=58;value_sum=1252.0;replicates=2 -chr1 repmatch . 65160 65161 615.4575949367088 . . median_distance=-4;value_sum=1236.0;replicates=2 -chr1 repmatch . 151365 151366 592.5522151898734 . . median_distance=-28;value_sum=1190.0;replicates=2 -chr1 repmatch . 108611 108612 570.6427215189874 . . median_distance=-45;value_sum=1146.0;replicates=2 -chr1 repmatch . 106047 106048 569.646835443038 . . median_distance=7;value_sum=1144.0;replicates=2 -chr1 repmatch . 481 482 682.2006329113924 . . median_distance=-7;value_sum=1371.0;replicates=2 -chr1 repmatch . 59228 59229 562.6756329113924 . . median_distance=56;value_sum=1130.0;replicates=2 -chr1 repmatch . 173276 173277 543.7537974683544 . . median_distance=8;value_sum=1092.0;replicates=2 -chr1 repmatch . 434 435 431.5107594936709 . . median_distance=43;value_sum=866.0;replicates=2 -chr1 repmatch . 45670 45671 490.971835443038 . . median_distance=-35;value_sum=986.0;replicates=2 -chr1 repmatch . 31670 31671 487.9841772151899 . . median_distance=66;value_sum=980.0;replicates=2 -chr1 repmatch . 32483 32484 476.0335443037975 . . median_distance=48;value_sum=956.0;replicates=2 -chr1 repmatch . 6714 6715 431.218670886076 . . median_distance=-4;value_sum=866.0;replicates=2 -chr1 repmatch . 136369 136370 363.498417721519 . . median_distance=-14;value_sum=730.0;replicates=2 -chr1 repmatch . 39237 39238 360.5107594936709 . . median_distance=61;value_sum=724.0;replicates=2 -chr1 repmatch . 668 669 317.6876582278481 . . median_distance=-48;value_sum=638.0;replicates=2 -chr1 repmatch . 98551 98552 121.49810126582278 . . median_distance=27;value_sum=244.0;replicates=2 -chr1 repmatch . 180331 180332 96.60094936708862 . . median_distance=82;value_sum=194.0;replicates=2 -chr1 repmatch . 230172 230173 42.87658227848101 . . median_distance=-2;value_sum=86.0;replicates=2 -chr1 repmatch . 230133 230134 26.95886075949367 . . median_distance=-8;value_sum=54.0;replicates=2 -chr1 repmatch . 230154 230155 44.69145569620253 . . median_distance=34;value_sum=90.0;replicates=2 -chr1 repmatch . 96919 96920 11.950632911392404 . . median_distance=3;value_sum=24.0;replicates=2 -chr1 repmatch . 197535 197536 4.9794303797468356 . . median_distance=73;value_sum=10.0;replicates=2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unmatched_peaks_out1.tabular Wed Dec 16 14:45:32 2015 -0500 @@ -0,0 +1,3 @@ +chrom midpoint midpoint+1 c-w sum c-w distance replicate id +chr1 388 389 359.0 20 1 +chr1 72731 72732 710.0 100 1
--- a/tool_dependencies.xml Wed Dec 02 20:32:21 2015 -0500 +++ b/tool_dependencies.xml Wed Dec 16 14:45:32 2015 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="anaconda" version="2.3.0"> - <repository changeset_revision="1da77309352e" name="package_anaconda_2_3_0" owner="greg" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="d3f29b11da06" name="package_anaconda_2_3_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>