Mercurial > repos > iuc > cwpair2
changeset 5:71188f3f4b76 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cwpair2 commit cb490a0eee9efc2cd6c98d5bb714b75b5894c56c
| author | iuc |
|---|---|
| date | Mon, 06 Nov 2017 23:19:50 -0500 |
| parents | d843468aeb8f |
| children | c4b926c9831c |
| files | cwpair2.xml cwpair2_macros.xml cwpair2_util.py cwpair2_util.pyc test-data/mode_d_output2.tabular test-data/mode_mp_output1.gff test-data/mode_mp_output2.gff test-data/statistics1.tabular test-data/statistics2.tabular |
| diffstat | 9 files changed, 215 insertions(+), 226 deletions(-) [+] |
line wrap: on
line diff
--- a/cwpair2.xml Sat Jan 21 14:40:25 2017 -0500 +++ b/cwpair2.xml Mon Nov 06 23:19:50 2017 -0500 @@ -5,32 +5,30 @@ <import>cwpair2_macros.xml</import> </macros> <expand macro="requirements" /> - <command detect_errors="aggressive"> - <![CDATA[ - python $__tool_directory__/cwpair2.py - #for $i in $input: - --input "${i}" "${i.hid}" - #end for - --up_distance $up_distance - --down_distance $down_distance - --method $method - --binsize $binsize - --threshold_format $threshold_format_cond.threshold_format - #if str($threshold_format_cond.threshold_format) == "absolute_threshold": - --absolute_threshold $threshold_format_cond.absolute_threshold - #elif str($threshold_format_cond.threshold_format) == "relative_threshold": - --relative_threshold $threshold_format_cond.relative_threshold - #end if - --output_files $output_files - --statistics_output "$statistics_output" - ]]> - </command> + <command detect_errors="aggressive"><![CDATA[ +python '$__tool_directory__/cwpair2.py' +#for $i in $input: + --input '${i}' '${i.hid}' +#end for +--up_distance $up_distance +--down_distance $down_distance +--method $method +--binsize $binsize +--threshold_format $threshold_format_cond.threshold_format +#if str($threshold_format_cond.threshold_format) == "absolute_threshold": + --absolute_threshold $threshold_format_cond.absolute_threshold +#elif str($threshold_format_cond.threshold_format) == "relative_threshold": + --relative_threshold $threshold_format_cond.relative_threshold +#end if +--output_files $output_files +--statistics_output '$statistics_output' + ]]></command> <inputs> - <param name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" /> + <param name="input" type="data" format="gff" multiple="true" label="Find matched pairs on" /> <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" help="The maximum distance upstream or 5’ to the primary peak"/> <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" help="The maximum distance downstream or 3’ to the primary peak"/> <param name="method" type="select" label="Method of finding a match"> - <option value="mode" selected="True">Mode</option> + <option value="mode" selected="true">Mode</option> <option value="closest">Closest</option> <option value="largest">Largest</option> <option value="all">All</option> @@ -179,7 +177,6 @@ * **closest/largest/mode P** - pdf file that provides the preview plots graph (the initial iteration of the process for finding the mode). * **closest/largest/mode F** - pdf file that provides the final plots graph. * **Statistics Table** - provides the number of peaks in pairs (dividing this by 2 provides the number of peak-pairs). - </help> <expand macro="citations" /> </tool>
--- a/cwpair2_macros.xml Sat Jan 21 14:40:25 2017 -0500 +++ b/cwpair2_macros.xml Mon Nov 06 23:19:50 2017 -0500 @@ -6,14 +6,6 @@ <requirement type="package" version="1.5.3">matplotlib</requirement> </requirements> </xml> - <xml name="stdio"> - <stdio> - <exit_code range="1:"/> - <exit_code range=":-1"/> - <regex match="Error:"/> - <regex match="Exception:"/> - </stdio> - </xml> <xml name="citations"> <citations> <citation type="bibtex">
--- a/cwpair2_util.py Sat Jan 21 14:40:25 2017 -0500 +++ b/cwpair2_util.py Mon Nov 06 23:19:50 2017 -0500 @@ -6,7 +6,7 @@ import matplotlib matplotlib.use('Agg') -from matplotlib import pyplot # noqa: E402 +from matplotlib import pyplot # noqa: I202,E402 # Data outputs DETAILS = 'D' @@ -92,7 +92,7 @@ def parse_chromosomes(reader): # This version of cwpair2 accepts only gff format as input. chromosomes = {} - reader.next() + next(reader) for line in reader: cname, junk, junk, start, end, value, strand, junk, junk = line start = int(start) @@ -245,7 +245,7 @@ if output_files == 'all' and method == 'all': frequency_plot([s['dist'] for s in statistics], statistics[0]['graph_path'], - labels=METHODS.keys()) + labels=list(METHODS.keys())) return statistics
--- a/test-data/mode_d_output2.tabular Sat Jan 21 14:40:25 2017 -0500 +++ b/test-data/mode_d_output2.tabular Mon Nov 06 23:19:50 2017 -0500 @@ -1,67 +1,67 @@ chrom start end value strand chrom start end value strand midpoint c-w reads sum c-w distance (bp) -chr1 87147 87167 3492.0 + chr1 87198 87218 2207.0 - 87182 5699.0 51 -chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52 -chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2 -chr1 255 275 2810.0 + chr1 323 343 486.0 - 299 3296.0 68 -chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59 -chr1 86954 86974 1948.0 + chr1 86991 87011 65.0 - 86982 2013.0 37 -chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43 -chr1 87171 87191 1436.0 + chr1 87234 87254 637.0 - 87212 2073.0 63 -chr1 201 221 1411.0 + chr1 261 281 1278.0 - 241 2689.0 60 -chr1 229741 229761 1380.0 + chr1 229784 229804 615.0 - 229772 1995.0 43 -chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46 -chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29 -chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0 -chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37 -chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12 -chr1 231 251 1146.0 + chr1 279 299 1328.0 - 265 2474.0 48 -chr1 87098 87118 1125.0 + chr1 87158 87178 2039.0 - 87138 3164.0 60 -chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91 -chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99 -chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44 -chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15 -chr1 87019 87039 769.0 + chr1 87101 87121 1134.0 - 87070 1903.0 82 -chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43 -chr1 348 368 699.0 + chr1 410 430 8.0 - 389 707.0 62 -chr1 92543 92563 699.0 + chr1 92639 92659 2137.0 - 92601 2836.0 96 -chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4 -chr1 307 327 685.0 + chr1 373 393 200.0 - 350 885.0 66 -chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63 -chr1 87085 87105 676.0 + chr1 87049 87069 422.0 - 87077 1098.0 -36 -chr1 72781 72801 657.0 + chr1 72810 72830 212.0 - 72805 869.0 29 -chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2 -chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4 -chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7 -chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83 -chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48 -chr1 160 180 451.0 + chr1 215 235 2611.0 - 197 3062.0 55 -chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4 -chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20 -chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58 -chr1 438 458 334.0 + chr1 468 488 468.0 - 463 802.0 30 -chr1 72671 72691 304.0 + chr1 72771 72791 406.0 - 72731 710.0 100 -chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10 -chr1 92631 92651 260.0 + chr1 92664 92684 187.0 - 92657 447.0 33 -chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14 -chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45 -chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35 -chr1 368 388 192.0 + chr1 446 466 170.0 - 417 362.0 78 -chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48 -chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56 -chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100 -chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86 -chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61 -chr1 229721 229741 84.0 + chr1 229757 229777 3151.0 - 229749 3235.0 36 -chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41 -chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25 -chr1 230110 230130 42.0 + chr1 230173 230193 33.0 - 230151 75.0 63 -chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66 -chr1 180280 180300 38.0 + chr1 180362 180382 59.0 - 180331 97.0 82 -chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27 -chr1 230163 230183 23.0 + chr1 230150 230170 7.0 - 230166 30.0 -13 -chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8 -chr1 230145 230165 8.0 + chr1 230132 230152 2.0 - 230148 10.0 -13 -chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51 -chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30 -chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73 -chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3 +chr1 87147 87167 3492.0 + chr1 87158 87178 2039.0 - 87162 5531.0 11.0 +chr1 87 107 3211.0 + chr1 139 159 993.0 - 123 4204.0 52.0 +chr1 48 68 2842.0 + chr1 50 70 39.0 - 59 2881.0 2.0 +chr1 255 275 2810.0 + chr1 279 299 1328.0 - 277 4138.0 24.0 +chr1 117 137 2163.0 + chr1 176 196 14.0 - 156 2177.0 59.0 +chr1 86954 86974 1948.0 + chr1 86991 87011 65.0 - 86982 2013.0 37.0 +chr1 169107 169127 1811.0 + chr1 169064 169084 76.0 - 169095 1887.0 -43.0 +chr1 87171 87191 1436.0 + chr1 87198 87218 2207.0 - 87194 3643.0 27.0 +chr1 201 221 1411.0 + chr1 215 235 2611.0 - 218 4022.0 14.0 +chr1 229741 229761 1380.0 + chr1 229757 229777 3151.0 - 229759 4531.0 16.0 +chr1 185076 185096 1309.0 + chr1 185122 185142 62.0 - 185109 1371.0 46.0 +chr1 39081 39101 1268.0 + chr1 39052 39072 82.0 - 39076 1350.0 -29.0 +chr1 92411 92431 1252.0 + chr1 92411 92431 136.0 - 92421 1388.0 0.0 +chr1 203872 203892 1234.0 + chr1 203835 203855 242.0 - 203863 1476.0 -37.0 +chr1 70776 70796 1148.0 + chr1 70788 70808 998.0 - 70792 2146.0 12.0 +chr1 231 251 1146.0 + chr1 261 281 1278.0 - 256 2424.0 30.0 +chr1 87098 87118 1125.0 + chr1 87101 87121 1134.0 - 87109 2259.0 3.0 +chr1 6163 6183 1049.0 + chr1 6254 6274 1076.0 - 6218 2125.0 91.0 +chr1 25246 25266 995.0 + chr1 25345 25365 188.0 - 25305 1183.0 99.0 +chr1 101411 101431 973.0 + chr1 101367 101387 1388.0 - 101399 2361.0 -44.0 +chr1 139213 139233 965.0 + chr1 139228 139248 214.0 - 139230 1179.0 15.0 +chr1 87019 87039 769.0 + chr1 87049 87069 422.0 - 87044 1191.0 30.0 +chr1 124318 124338 749.0 + chr1 124275 124295 12.0 - 124306 761.0 -43.0 +chr1 348 368 699.0 + chr1 373 393 200.0 - 370 899.0 25.0 +chr1 92543 92563 699.0 + chr1 92571 92591 90.0 - 92567 789.0 28.0 +chr1 138868 138888 698.0 + chr1 138864 138884 13.0 - 138876 711.0 -4.0 +chr1 307 327 685.0 + chr1 323 343 486.0 - 325 1171.0 16.0 +chr1 6413 6433 682.0 + chr1 6476 6496 567.0 - 6454 1249.0 63.0 +chr1 72781 72801 657.0 + chr1 72810 72830 212.0 - 72805 869.0 29.0 +chr1 22571 22591 609.0 + chr1 22569 22589 254.0 - 22580 863.0 -2.0 +chr1 65152 65172 575.0 + chr1 65148 65168 43.0 - 65160 618.0 -4.0 +chr1 106034 106054 558.0 + chr1 106041 106061 14.0 - 106047 572.0 7.0 +chr1 155028 155048 522.0 + chr1 155111 155131 1051.0 - 155079 1573.0 83.0 +chr1 32449 32469 476.0 + chr1 32497 32517 2.0 - 32483 478.0 48.0 +chr1 6706 6726 431.0 + chr1 6702 6722 2.0 - 6714 433.0 -4.0 +chr1 113782 113802 420.0 + chr1 113762 113782 296.0 - 113782 716.0 -20.0 +chr1 228633 228653 371.0 + chr1 228691 228711 255.0 - 228672 626.0 58.0 +chr1 438 458 334.0 + chr1 446 466 170.0 - 452 504.0 8.0 +chr1 72671 72691 304.0 + chr1 72771 72791 406.0 - 72731 710.0 100.0 +chr1 170119 170139 284.0 + chr1 170129 170149 373.0 - 170134 657.0 10.0 +chr1 92631 92651 260.0 + chr1 92639 92659 2137.0 - 92645 2397.0 8.0 +chr1 136366 136386 248.0 + chr1 136352 136372 117.0 - 136369 365.0 -14.0 +chr1 108624 108644 206.0 + chr1 108579 108599 367.0 - 108611 573.0 -45.0 +chr1 45678 45698 198.0 + chr1 45643 45663 295.0 - 45670 493.0 -35.0 +chr1 368 388 192.0 + chr1 388 408 167.0 - 388 359.0 20.0 +chr1 682 702 168.0 + chr1 634 654 151.0 - 668 319.0 -48.0 +chr1 59190 59210 168.0 + chr1 59246 59266 397.0 - 59228 565.0 56.0 +chr1 134170 134190 151.0 + chr1 134270 134290 508.0 - 134230 659.0 100.0 +chr1 55495 55515 125.0 + chr1 55581 55601 831.0 - 55548 956.0 86.0 +chr1 512 532 101.0 + chr1 468 488 468.0 - 500 569.0 -44.0 +chr1 39197 39217 101.0 + chr1 39258 39278 261.0 - 39237 362.0 61.0 +chr1 229721 229741 84.0 + chr1 229784 229804 615.0 - 229762 699.0 63.0 +chr1 116660 116680 74.0 + chr1 116619 116639 699.0 - 116649 773.0 -41.0 +chr1 19216 19236 42.0 + chr1 19191 19211 736.0 - 19213 778.0 -25.0 +chr1 230110 230130 42.0 + chr1 230132 230152 2.0 - 230131 44.0 22.0 +chr1 31627 31647 40.0 + chr1 31693 31713 450.0 - 31670 490.0 66.0 +chr1 180280 180300 38.0 + chr1 180272 180292 25.0 - 180286 63.0 -8.0 +chr1 98528 98548 34.0 + chr1 98555 98575 88.0 - 98551 122.0 27.0 +chr1 230163 230183 23.0 + chr1 230173 230193 33.0 - 230178 56.0 10.0 +chr1 173262 173282 11.0 + chr1 173270 173290 535.0 - 173276 546.0 8.0 +chr1 230145 230165 8.0 + chr1 230150 230170 7.0 - 230157 15.0 5.0 +chr1 95920 95940 5.0 + chr1 95971 95991 684.0 - 95955 689.0 51.0 +chr1 199418 199438 5.0 + chr1 199388 199408 805.0 - 199413 810.0 -30.0 +chr1 197489 197509 3.0 + chr1 197562 197582 2.0 - 197535 5.0 73.0 +chr1 96908 96928 2.0 + chr1 96911 96931 10.0 - 96919 12.0 3.0 +chr1 151369 151389 2.0 + chr1 151341 151361 593.0 - 151365 595.0 -28.0
--- a/test-data/mode_mp_output1.gff Sat Jan 21 14:40:25 2017 -0500 +++ b/test-data/mode_mp_output1.gff Mon Nov 06 23:19:50 2017 -0500 @@ -1,56 +1,56 @@ -chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 299 300 3296.0 . . cw_distance=68 -chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36 -chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60 -chr1 cwpair . 197 198 3062.0 . . cw_distance=55 -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 -chr1 cwpair . 241 242 2689.0 . . cw_distance=60 -chr1 cwpair . 265 266 2474.0 . . cw_distance=48 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 87212 87213 2073.0 . . cw_distance=63 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 -chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43 -chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 87035 87036 972.0 . . cw_distance=47 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 350 351 885.0 . . cw_distance=66 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 463 464 802.0 . . cw_distance=30 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 -chr1 cwpair . 389 390 707.0 . . cw_distance=62 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 417 418 362.0 . . cw_distance=78 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 627 628 247.0 . . cw_distance=33 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 -chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 230148 230149 10.0 . . cw_distance=-13 +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11.0 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16.0 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 +chr1 cwpair . 277 278 4138.0 . . cw_distance=24.0 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14.0 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27.0 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 +chr1 cwpair . 256 257 2424.0 . . cw_distance=30.0 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8.0 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3.0 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59.0 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37.0 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30.0 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16.0 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 +chr1 cwpair . 370 371 899.0 . . cw_distance=25.0 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29.0 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28.0 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100.0 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63.0 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 +chr1 cwpair . 477 478 566.0 . . cw_distance=1.0 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 +chr1 cwpair . 452 453 504.0 . . cw_distance=8.0 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14.0 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61.0 +chr1 cwpair . 388 389 359.0 . . cw_distance=20.0 +chr1 cwpair . 627 628 247.0 . . cw_distance=33.0 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27.0 +chr1 cwpair . 180286 180287 63.0 . . cw_distance=-8.0 +chr1 cwpair . 230178 230179 56.0 . . cw_distance=10.0 +chr1 cwpair . 230131 230132 44.0 . . cw_distance=22.0 +chr1 cwpair . 230157 230158 15.0 . . cw_distance=5.0 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3.0 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73.0
--- a/test-data/mode_mp_output2.gff Sat Jan 21 14:40:25 2017 -0500 +++ b/test-data/mode_mp_output2.gff Mon Nov 06 23:19:50 2017 -0500 @@ -1,66 +1,66 @@ -chr1 cwpair . 87182 87183 5699.0 . . cw_distance=51 -chr1 cwpair . 123 124 4204.0 . . cw_distance=52 -chr1 cwpair . 299 300 3296.0 . . cw_distance=68 -chr1 cwpair . 229749 229750 3235.0 . . cw_distance=36 -chr1 cwpair . 87138 87139 3164.0 . . cw_distance=60 -chr1 cwpair . 197 198 3062.0 . . cw_distance=55 -chr1 cwpair . 59 60 2881.0 . . cw_distance=2 -chr1 cwpair . 92601 92602 2836.0 . . cw_distance=96 -chr1 cwpair . 241 242 2689.0 . . cw_distance=60 -chr1 cwpair . 265 266 2474.0 . . cw_distance=48 -chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44 -chr1 cwpair . 156 157 2177.0 . . cw_distance=59 -chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12 -chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91 -chr1 cwpair . 87212 87213 2073.0 . . cw_distance=63 -chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37 -chr1 cwpair . 229772 229773 1995.0 . . cw_distance=43 -chr1 cwpair . 87070 87071 1903.0 . . cw_distance=82 -chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43 -chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83 -chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37 -chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0 -chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46 -chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29 -chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63 -chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99 -chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15 -chr1 cwpair . 87077 87078 1098.0 . . cw_distance=-36 -chr1 cwpair . 55548 55549 956.0 . . cw_distance=86 -chr1 cwpair . 350 351 885.0 . . cw_distance=66 -chr1 cwpair . 72805 72806 869.0 . . cw_distance=29 -chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2 -chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30 -chr1 cwpair . 463 464 802.0 . . cw_distance=30 -chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25 -chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41 -chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43 -chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20 -chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4 -chr1 cwpair . 72731 72732 710.0 . . cw_distance=100 -chr1 cwpair . 389 390 707.0 . . cw_distance=62 -chr1 cwpair . 95955 95956 689.0 . . cw_distance=51 -chr1 cwpair . 134230 134231 659.0 . . cw_distance=100 -chr1 cwpair . 170134 170135 657.0 . . cw_distance=10 -chr1 cwpair . 228672 228673 626.0 . . cw_distance=58 -chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4 -chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28 -chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45 -chr1 cwpair . 106047 106048 572.0 . . cw_distance=7 -chr1 cwpair . 59228 59229 565.0 . . cw_distance=56 -chr1 cwpair . 173276 173277 546.0 . . cw_distance=8 -chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35 -chr1 cwpair . 31670 31671 490.0 . . cw_distance=66 -chr1 cwpair . 32483 32484 478.0 . . cw_distance=48 -chr1 cwpair . 92657 92658 447.0 . . cw_distance=33 -chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4 -chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14 -chr1 cwpair . 417 418 362.0 . . cw_distance=78 -chr1 cwpair . 39237 39238 362.0 . . cw_distance=61 -chr1 cwpair . 668 669 319.0 . . cw_distance=-48 -chr1 cwpair . 98551 98552 122.0 . . cw_distance=27 -chr1 cwpair . 180331 180332 97.0 . . cw_distance=82 -chr1 cwpair . 230151 230152 75.0 . . cw_distance=63 -chr1 cwpair . 230166 230167 30.0 . . cw_distance=-13 -chr1 cwpair . 96919 96920 12.0 . . cw_distance=3 -chr1 cwpair . 230148 230149 10.0 . . cw_distance=-13 +chr1 cwpair . 87162 87163 5531.0 . . cw_distance=11.0 +chr1 cwpair . 229759 229760 4531.0 . . cw_distance=16.0 +chr1 cwpair . 123 124 4204.0 . . cw_distance=52.0 +chr1 cwpair . 277 278 4138.0 . . cw_distance=24.0 +chr1 cwpair . 218 219 4022.0 . . cw_distance=14.0 +chr1 cwpair . 87194 87195 3643.0 . . cw_distance=27.0 +chr1 cwpair . 59 60 2881.0 . . cw_distance=2.0 +chr1 cwpair . 256 257 2424.0 . . cw_distance=30.0 +chr1 cwpair . 92645 92646 2397.0 . . cw_distance=8.0 +chr1 cwpair . 101399 101400 2361.0 . . cw_distance=-44.0 +chr1 cwpair . 87109 87110 2259.0 . . cw_distance=3.0 +chr1 cwpair . 156 157 2177.0 . . cw_distance=59.0 +chr1 cwpair . 70792 70793 2146.0 . . cw_distance=12.0 +chr1 cwpair . 6218 6219 2125.0 . . cw_distance=91.0 +chr1 cwpair . 86982 86983 2013.0 . . cw_distance=37.0 +chr1 cwpair . 169095 169096 1887.0 . . cw_distance=-43.0 +chr1 cwpair . 155079 155080 1573.0 . . cw_distance=83.0 +chr1 cwpair . 203863 203864 1476.0 . . cw_distance=-37.0 +chr1 cwpair . 92421 92422 1388.0 . . cw_distance=0.0 +chr1 cwpair . 185109 185110 1371.0 . . cw_distance=46.0 +chr1 cwpair . 39076 39077 1350.0 . . cw_distance=-29.0 +chr1 cwpair . 6454 6455 1249.0 . . cw_distance=63.0 +chr1 cwpair . 87044 87045 1191.0 . . cw_distance=30.0 +chr1 cwpair . 25305 25306 1183.0 . . cw_distance=99.0 +chr1 cwpair . 139230 139231 1179.0 . . cw_distance=15.0 +chr1 cwpair . 325 326 1171.0 . . cw_distance=16.0 +chr1 cwpair . 55548 55549 956.0 . . cw_distance=86.0 +chr1 cwpair . 370 371 899.0 . . cw_distance=25.0 +chr1 cwpair . 72805 72806 869.0 . . cw_distance=29.0 +chr1 cwpair . 22580 22581 863.0 . . cw_distance=-2.0 +chr1 cwpair . 199413 199414 810.0 . . cw_distance=-30.0 +chr1 cwpair . 92567 92568 789.0 . . cw_distance=28.0 +chr1 cwpair . 19213 19214 778.0 . . cw_distance=-25.0 +chr1 cwpair . 116649 116650 773.0 . . cw_distance=-41.0 +chr1 cwpair . 124306 124307 761.0 . . cw_distance=-43.0 +chr1 cwpair . 113782 113783 716.0 . . cw_distance=-20.0 +chr1 cwpair . 138876 138877 711.0 . . cw_distance=-4.0 +chr1 cwpair . 72731 72732 710.0 . . cw_distance=100.0 +chr1 cwpair . 229762 229763 699.0 . . cw_distance=63.0 +chr1 cwpair . 95955 95956 689.0 . . cw_distance=51.0 +chr1 cwpair . 134230 134231 659.0 . . cw_distance=100.0 +chr1 cwpair . 170134 170135 657.0 . . cw_distance=10.0 +chr1 cwpair . 228672 228673 626.0 . . cw_distance=58.0 +chr1 cwpair . 65160 65161 618.0 . . cw_distance=-4.0 +chr1 cwpair . 151365 151366 595.0 . . cw_distance=-28.0 +chr1 cwpair . 108611 108612 573.0 . . cw_distance=-45.0 +chr1 cwpair . 106047 106048 572.0 . . cw_distance=7.0 +chr1 cwpair . 500 501 569.0 . . cw_distance=-44.0 +chr1 cwpair . 59228 59229 565.0 . . cw_distance=56.0 +chr1 cwpair . 173276 173277 546.0 . . cw_distance=8.0 +chr1 cwpair . 452 453 504.0 . . cw_distance=8.0 +chr1 cwpair . 45670 45671 493.0 . . cw_distance=-35.0 +chr1 cwpair . 31670 31671 490.0 . . cw_distance=66.0 +chr1 cwpair . 32483 32484 478.0 . . cw_distance=48.0 +chr1 cwpair . 6714 6715 433.0 . . cw_distance=-4.0 +chr1 cwpair . 136369 136370 365.0 . . cw_distance=-14.0 +chr1 cwpair . 39237 39238 362.0 . . cw_distance=61.0 +chr1 cwpair . 388 389 359.0 . . cw_distance=20.0 +chr1 cwpair . 668 669 319.0 . . cw_distance=-48.0 +chr1 cwpair . 98551 98552 122.0 . . cw_distance=27.0 +chr1 cwpair . 180286 180287 63.0 . . cw_distance=-8.0 +chr1 cwpair . 230178 230179 56.0 . . cw_distance=10.0 +chr1 cwpair . 230131 230132 44.0 . . cw_distance=22.0 +chr1 cwpair . 230157 230158 15.0 . . cw_distance=5.0 +chr1 cwpair . 96919 96920 12.0 . . cw_distance=3.0 +chr1 cwpair . 197535 197536 5.0 . . cw_distance=73.0
--- a/test-data/statistics1.tabular Sat Jan 21 14:40:25 2017 -0500 +++ b/test-data/statistics1.tabular Mon Nov 06 23:19:50 2017 -0500 @@ -1,4 +1,4 @@ fname final_mode preview_mode perc95 paired orphans -mode: data 1 63.5 63.5 1437.0 114 384 -closest: data 1 10.5 NA 1437.0 112 386 +mode: data 1 -3.5 16.5 1437.0 112 386 +closest: data 1 -3.5 NA 1437.0 112 386 largest: data 1 -3.5 NA 1437.0 110 388
--- a/test-data/statistics2.tabular Sat Jan 21 14:40:25 2017 -0500 +++ b/test-data/statistics2.tabular Mon Nov 06 23:19:50 2017 -0500 @@ -1,4 +1,4 @@ fname final_mode preview_mode perc95 paired orphans -mode: data 1 63.5 63.5 1437.0 134 364 -closest: data 1 8.5 NA 1437.0 132 366 +mode: data 1 -3.5 16.5 1437.0 132 366 +closest: data 1 -3.5 NA 1437.0 132 366 largest: data 1 -24.5 NA 1437.0 128 370