# HG changeset patch # User eric-rasche # Date 1498819718 14400 # Node ID e6440d0201f79ee1602327724a4c47e0eaa2aa06 # Parent eb3af6e9f6337f60e764bd64a18bd95802c8b43e planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7e335df423e3e06da3d33a5378a336a149e6cc6c diff -r eb3af6e9f633 -r e6440d0201f7 circos/circos.png Binary file circos/circos.png has changed diff -r eb3af6e9f633 -r e6440d0201f7 circos/circos.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/circos.svg Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,297 @@ + + + + + + + + +0 + +0 kb + + + + + +5 kb + + + + + +10 kb + + + + + +15 kb + + + + + +20 kb + + + + + +25 kb + + + + + +30 kb + + + + + +35 kb + + + + + +40 kb + + + + + +45 kb + + + + + +50 kb + +1 + +0 kb + + + + + +5 kb + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r eb3af6e9f633 -r e6440d0201f7 circos/conf/2d.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/conf/2d.conf Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,31 @@ + + + type = tile + file = data/data-1.txt + + r1 = 0.95r + r0 = 0.7r + orientation = in + + + stroke_thickness = 1 + layers = 20 + thickness = 15.0 + padding = 2.0 + + layers_overflow = collapse + + + + + condition = 1 + color = eval(sprintf("brbg-15-div-%d", remap_int(var(value), 0.0, 12000.0, 1, 15))) + + + + + + + + + diff -r eb3af6e9f633 -r e6440d0201f7 circos/conf/circos.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/conf/circos.conf Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,21 @@ + +<> +<> +karyotype = karyotype.txt + + + <> + + +<> +<> + + <> + <> + + + <> + + +<> + \ No newline at end of file diff -r eb3af6e9f633 -r e6440d0201f7 circos/conf/galaxy_test_case.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/conf/galaxy_test_case.xml Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r eb3af6e9f633 -r e6440d0201f7 circos/conf/highlight.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/conf/highlight.conf Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,2 @@ + + \ No newline at end of file diff -r eb3af6e9f633 -r e6440d0201f7 circos/conf/ideogram.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/conf/ideogram.conf Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,23 @@ + + + + + + default = 0.005r + + + # ideogram position, thickness and fill + radius = 0.9r + thickness = 10.0p + fill = yes + + show_label = yes + label_radius = dims(ideogram,radius) + 0.075r + label_size = 24 + label_parallel = yes + + show_bands = yes + fill_bands = yes + band_transparency = 4 + + diff -r eb3af6e9f633 -r e6440d0201f7 circos/conf/karyotype.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/conf/karyotype.txt Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,2 @@ +chr - ctgA 0 0 50001 set3-12-qual-1 +chr - ctgB 1 0 6079 set3-12-qual-2 diff -r eb3af6e9f633 -r e6440d0201f7 circos/conf/links.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/conf/links.conf Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,2 @@ + + \ No newline at end of file diff -r eb3af6e9f633 -r e6440d0201f7 circos/conf/plot_highlight.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/conf/plot_highlight.conf Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,2 @@ + + \ No newline at end of file diff -r eb3af6e9f633 -r e6440d0201f7 circos/conf/ticks.conf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/conf/ticks.conf Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,32 @@ + +show_ticks = yes +show_tick_labels = yes + + + + + radius = 1.0r + color = 0, 0, 0 + + thickness = 2p + multiplier = 0.001 + + + spacing = 5000.0 + size = 10.0p + show_label = yes + label_size = 20.0p + label_offset = 10.0p + format = %d kb + + + spacing = 1000.0 + size = 5.0p + show_label = no + label_size = 20.0p + label_offset = 10.0p + format = %d kb + + + + \ No newline at end of file diff -r eb3af6e9f633 -r e6440d0201f7 circos/data/data-0.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/data/data-0.txt Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,499 @@ +ctgA 1 19 -0.506365641109759 +ctgA 101 119 -0.873297297213995 +ctgA 201 219 -0.999755839901149 +ctgA 301 319 -0.850919359639177 +ctgA 401 419 -0.467771805322476 +ctgA 501 519 0.0441824483318732 +ctgA 601 619 0.543970523363376 +ctgA 701 719 0.893969648197021 +ctgA 801 819 0.99780327442197 +ctgA 901 919 0.826879540532003 +ctgA 1001 1019 0.428264391396659 +ctgA 1101 1119 -0.0882786064717262 +ctgA 1201 1219 -0.580513008156313 +ctgA 1301 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0.979566222305013 +ctgA 39901 39919 0.946539656785734 +ctgA 40001 40019 0.652871796525078 +ctgA 40101 40119 0.179427685870145 +ctgA 40201 40219 -0.343424037051613 +ctgA 40301 40319 -0.771709742563807 +ctgA 40401 40419 -0.987495712830468 +ctgA 40501 40519 -0.931362636389977 +ctgA 40601 40619 -0.618767443774911 +ctgA 40701 40719 -0.13578705225865 +ctgA 40801 40819 0.384583968225014 +ctgA 40901 40919 0.799055079818084 +ctgA 41001 41019 0.993496582423937 +ctgA 41101 41119 0.91436662533687 +ctgA 41201 41219 0.583454612012034 +ctgA 41301 41319 0.0918812207856598 +ctgA 41401 41419 -0.424992790627422 +ctgA 41501 41519 -0.824839828674128 +ctgA 41601 41619 -0.997557111133059 +ctgA 41701 41719 -0.895584817555511 +ctgA 41801 41819 -0.547002268691819 +ctgA 41901 41919 -0.0477959413987577 +ctgA 42001 42019 0.464571584118009 +ctgA 42101 42119 0.849013630425847 +ctgA 42201 42219 0.999669368573369 +ctgA 42301 42319 0.87505389471161 +ctgA 42401 42419 0.509481606783953 +ctgA 42501 42519 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-0.980995619897873 +ctgA 45301 45319 -0.747680972860835 +ctgA 45401 45419 -0.308483206798754 +ctgA 45501 45519 0.215659190848055 +ctgA 45601 45619 0.680417187299892 +ctgA 45701 45719 0.957813972427147 +ctgA 45801 45819 0.971464941829636 +ctgA 45901 45919 0.717611133783957 +ctgA 46001 46019 0.266154305421701 +ctgA 46101 46119 -0.258591372772452 +ctgA 46201 46219 -0.71213074732663 +ctgA 46301 46319 -0.969576193139719 +ctgA 46401 46419 -0.960036951603826 +ctgA 46501 46519 -0.686139769783315 +ctgA 46601 46619 -0.223305593418733 +ctgA 46701 46719 0.301018514798568 +ctgA 46801 46819 0.742453485856362 +ctgA 46901 46919 0.979444790500868 +ctgA 47001 47019 0.946733968569148 +ctgA 47101 47119 0.653328345765115 +ctgA 47201 47219 0.180020756138357 +ctgA 47301 47319 -0.342857754921908 +ctgA 47401 47419 -0.77132618129705 +ctgA 47501 47519 -0.987400490722168 +ctgA 47601 47619 -0.931581974014641 +ctgA 47701 47719 -0.619240943829511 +ctgA 47801 47819 -0.13638433070021 +ctgA 47901 47919 0.38402737933528 +ctgA 48001 48019 0.798692444052197 +ctgA 48101 48119 0.993427755984289 +ctgA 48201 48219 0.914610560427116 +ctgA 48301 48319 0.583944138115545 +ctgA 48401 48419 0.0924815408904855 +ctgA 48501 48519 -0.424446982019324 +ctgA 48601 48619 -0.824498826652114 +ctgA 48701 48719 -0.997514814783015 +ctgA 48801 48819 -0.895852873695781 +ctgA 48901 48919 -0.547506864779039 +ctgA 49001 49019 -0.048398130716271 +ctgA 49101 49119 0.464037621778865 +ctgA 49201 49219 0.848694928139091 +ctgA 49301 49319 0.99965368491949 +ctgA 49401 49419 0.875345548376914 +ctgA 49501 49519 0.51000028735736 +ctgA 49601 49619 0.00422019694387214 +ctgA 49701 49719 -0.502721976418416 +ctgA 49801 49819 -0.871233492502601 diff -r eb3af6e9f633 -r e6440d0201f7 circos/data/data-1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/circos/data/data-1.txt Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,201 @@ +ctgA 0 50001 strand=None,score=0.0,value=0.0,id=ctgA +ctgA 999 2000 strand=None,score=0.0,value=0.0,id=Remark:hga +ctgA 999 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31760 31984 strand=1,score=0.0,value=0.0,id=seg10 +ctgA 32009 32057 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 32207 32680 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 32328 32359 strand=1,score=0.0,value=0.0,id=seg01 +ctgA 32373 32937 strand=1,score=0.0,value=0.0,id=seg10 +ctgA 32594 32696 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 32891 32901 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 33052 33325 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 33126 33388 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 33324 35791 strand=1,score=0.0,value=0.0,id=m04 +ctgA 33437 33868 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 33438 33443 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 33758 34209 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 34243 34313 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 34400 34466 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 34604 34983 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 35332 35507 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 35641 35904 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 36033 38167 strand=1,score=100,value=100,id=f09 +ctgA 36615 37057 strand=-1,score=0.0,value=0.0,id=seg09 +ctgA 36648 40440 strand=-1,score=300,value=300,id=f03 +ctgA 37207 37227 strand=-1,score=0.0,value=0.0,id=seg09 +ctgA 37241 38653 strand=1,score=10,value=10,id=f04 +ctgA 37496 40559 strand=-1,score=0.0,value=0.0,id=m15 +ctgA 39264 39361 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 39752 40034 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 40514 40954 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 41136 41318 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 41251 41365 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 41491 41504 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 41753 41948 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 41940 42377 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 42056 42474 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 42747 42954 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 42889 43270 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 43394 43811 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 43400 43897 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 44042 44113 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 44064 44556 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 44190 44514 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 44398 44888 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 44551 45043 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 44704 47713 strand=-1,score=400,value=400,id=f01 +ctgA 44762 45030 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 45230 45488 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 45280 45375 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 45372 45600 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 45710 46041 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 45789 46022 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 45896 46315 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 46011 48851 strand=1,score=0.0,value=0.0,id=m09 +ctgA 46091 46318 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 46424 46564 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 46490 46890 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 46737 47087 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 46815 46992 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 46989 48410 strand=-1,score=100,value=100,id=f11 +ctgA 47125 47297 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 47328 47595 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 47448 47829 strand=-1,score=0.0,value=0.0,id=seg14 +ctgA 47734 47983 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 47857 47979 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 48168 48453 strand=-1,score=0.0,value=0.0,id=seg15 +ctgA 48252 48366 strand=1,score=0.0,value=0.0,id=m01 +ctgA 48446 48709 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 48930 49186 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 49405 49476 strand=1,score=0.0,value=0.0,id=seg13 +ctgA 49471 49699 strand=-1,score=0.0,value=0.0,id=seg07 +ctgA 49757 50000 strand=-1,score=3040,value=3040,id=f12 +ctgA 49761 50000 strand=1,score=0.0,value=0.0,id=seg13 +ctgA 49956 50000 strand=-1,score=0.0,value=0.0,id=seg07 +ctgB 0 6079 strand=None,score=0.0,value=0.0,id=ctgB +ctgB 1658 1984 strand=1,score=0.0,value=0.0,id=f07 +ctgB 3013 6130 strand=1,score=0.0,value=0.0,id=f06 +ctgB 4714 5968 strand=-1,score=0.0,value=0.0,id=f05 diff -r eb3af6e9f633 -r e6440d0201f7 generate_links.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_links.py Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,14 @@ +import random + +for i in range(50): + a = random.randint(0, 45000) + b = random.randint(0, 6000) + print(' '.join(map(str, [ + 'ctgA', + a, + a + random.randint(0, 5000), + 'ctgB', + b, + b + random.randint(0, 79), + 'value=%s' % random.randint(0, 1000), + ]))) diff -r eb3af6e9f633 -r e6440d0201f7 macros.xml --- a/macros.xml Sat Jun 10 16:21:01 2017 -0400 +++ b/macros.xml Fri Jun 30 06:48:38 2017 -0400 @@ -291,7 +291,20 @@ - + + + + + + + + + + + + + + diff -r eb3af6e9f633 -r e6440d0201f7 macros_conffiles.xml --- a/macros_conffiles.xml Sat Jun 10 16:21:01 2017 -0400 +++ b/macros_conffiles.xml Fri Jun 30 06:48:38 2017 -0400 @@ -110,7 +110,7 @@ extend_bin = ${data.plot_format.format_specific.extend_bins} fill_color = ${data.plot_format.format_specific.fill_color} #else if str($plot_type) == 'heatmap': - fill_color = $circosColor($data.plot_format.format_specific.fill_color) + color = $circosColor($data.plot_format.format_specific.fill_color) scale_log_base = ${data.plot_format.format_specific.scale_log_base} #else if str($plot_type) == 'line': color = $circosColor($data.plot_format.format_specific.color) @@ -145,19 +145,19 @@ #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ]) condition = $on_str #elif str($condition.application.application_select) == "pos": - #if $condition.application.pos_gt != 0: + #if float($condition.application.pos_gt) != 0: condition = var(start) > $condition.application.pos_gt #end if - #if $condition.application.pos_lt != 0: + #if float($condition.application.pos_lt) != 0: condition = var(start) < $condition.application.pos_lt #end if #elif str($condition.application.application_select) == "value": - #if $condition.application.pos_gt != 0: + #if float($condition.application.pos_gt) != 0: condition = var(value) > $condition.application.pos_gt #end if - #if $condition.application.pos_lt != 0: + #if float($condition.application.pos_lt) != 0: condition = var(value) < $condition.application.pos_lt #end if #elif str($condition.application.application_select) == "var": @@ -171,8 +171,9 @@ #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) #set x_min = $x_fill_color_count if $action.action.invert else 1 #set x_max = 1 if $action.action.invert else $x_fill_color_count + #set color_action = "fill_color" if str($plot_type) == 'histogram' else "color" - fill_color = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max}))) + $color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max}))) #else $action.action.action_select = ${action.action.action_value} #end if @@ -291,6 +292,15 @@ $actiontype = eval(sprintf("${action.action.dynamic.action_value}-%d", remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max}))) #end if + #elif $actiontype == 'z': + #if $action.action.dynamic.dynamic_select == "static": + #set actionval = $action.action.dynamic.action_value + $actiontype = $actionval + #else + #set x_min = 1000 if $action.action.dynamic.invert else 1 + #set x_max = 1 if $action.action.dynamic.invert else 1000 + $actiontype = eval(remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max})) + #end if #else #set actionval = $action.action.action_value $actiontype = $actionval diff -r eb3af6e9f633 -r e6440d0201f7 test-data/1/1.gff3 --- a/test-data/1/1.gff3 Sat Jun 10 16:21:01 2017 -0400 +++ b/test-data/1/1.gff3 Fri Jun 30 06:48:38 2017 -0400 @@ -25,171 +25,171 @@ ctgA example protein_coding_primary_transcript 1600 3000 . - . Name=Gene:hgb;Alias=hgb ctgA example polypeptide 1800 2900 . - . Name=Protein:HGB;Alias=hgb -ctgA example polypeptide_domain 11911 15561 . + . Name=m11;Note=kinase -ctgA example polypeptide_domain 13801 14007 . - . Name=m05;Note=helix loop helix -ctgA example polypeptide_domain 14731 17239 . - . Name=m14;Note=kinase -ctgA example polypeptide_domain 15396 16159 . + . Name=m03;Note=zinc finger -ctgA example polypeptide_domain 17023 17675 . + . Name=m08;Note=7-transmembrane -ctgA example polypeptide_domain 17667 17690 . + . Name=m13;Note=DEAD box -ctgA example polypeptide_domain 18048 18552 . - . Name=m07;Note=7-transmembrane -ctgA example polypeptide_domain 21748 25612 . + . Name=m12;Note=kinase -ctgA example polypeptide_domain 28332 30033 . - . Name=m02;Note=HOX -ctgA example polypeptide_domain 28342 28447 . - . Name=m10;Note=DEAD box -ctgA example polypeptide_domain 30578 31748 . + . Name=m06;Note=SUSHI repeat -ctgA example polypeptide_domain 33325 35791 . + . Name=m04;Note=Ig-like -ctgA example polypeptide_domain 37497 40559 . - . Name=m15;Note=7-transmembrane -ctgA example polypeptide_domain 46012 48851 . + . Name=m09;Note=kinase -ctgA example polypeptide_domain 48253 48366 . + . Name=m01;Note=WD40 +ctgA example polypeptide_domain 11911 15561 . + 502 Name=m11;Note=kinase +ctgA example polypeptide_domain 13801 14007 . - 415 Name=m05;Note=helix loop helix +ctgA example polypeptide_domain 14731 17239 . - 746 Name=m14;Note=kinase +ctgA example polypeptide_domain 15396 16159 . + 40 Name=m03;Note=zinc finger +ctgA example polypeptide_domain 17023 17675 . + 830 Name=m08;Note=7-transmembrane +ctgA example polypeptide_domain 17667 17690 . + 943 Name=m13;Note=DEAD box +ctgA example polypeptide_domain 18048 18552 . - 658 Name=m07;Note=7-transmembrane +ctgA example polypeptide_domain 21748 25612 . + 467 Name=m12;Note=kinase +ctgA example polypeptide_domain 28332 30033 . - 711 Name=m02;Note=HOX +ctgA example polypeptide_domain 28342 28447 . - 533 Name=m10;Note=DEAD box +ctgA example polypeptide_domain 30578 31748 . + 646 Name=m06;Note=SUSHI repeat +ctgA example polypeptide_domain 33325 35791 . + 479 Name=m04;Note=Ig-like +ctgA example polypeptide_domain 37497 40559 . - 711 Name=m15;Note=7-transmembrane +ctgA example polypeptide_domain 46012 48851 . + 533 Name=m09;Note=kinase +ctgA example polypeptide_domain 48253 48366 . + 646 Name=m01;Note=WD40 -ctgA example match 32329 32359 . + . Name=seg01 -ctgA example match 26122 26126 . + . Name=seg02 -ctgA example match 26497 26869 . + . Name=seg02 -ctgA example match 27201 27325 . + . Name=seg02 -ctgA example match 27372 27433 . + . Name=seg02 -ctgA example match 27565 27565 . + . Name=seg02 -ctgA example match 27813 28091 . + . Name=seg02 -ctgA example match 28093 28201 . + . Name=seg02 -ctgA example match 28329 28377 . + . Name=seg02 -ctgA example match 28829 29194 . + . Name=seg02 -ctgA example match 29517 29702 . + . Name=seg02 -ctgA example match 29713 30061 . + . Name=seg02 -ctgA example match 30329 30774 . + . Name=seg02 -ctgA example match 30808 31306 . + . Name=seg02 -ctgA example match 31516 31729 . + . Name=seg02 -ctgA example match 31753 32154 . + . Name=seg02 -ctgA example match 32595 32696 . + . Name=seg02 -ctgA example match 32892 32901 . + . Name=seg02 -ctgA example match 33127 33388 . + . Name=seg02 -ctgA example match 33439 33443 . + . Name=seg02 -ctgA example match 33759 34209 . + . Name=seg02 -ctgA example match 34401 34466 . + . Name=seg02 -ctgA example match 6885 7241 . - . Name=seg03 -ctgA example match 7410 7737 . - . Name=seg03 -ctgA example match 8055 8080 . - . Name=seg03 -ctgA example match 8306 8999 . - . Name=seg03 -ctgA example match 5233 5302 . - . Name=seg04 -ctgA example match 5800 6101 . - . Name=seg04 -ctgA example match 6442 6854 . - . Name=seg04 -ctgA example match 7106 7211 . - . Name=seg04 -ctgA example match 7695 8177 . - . Name=seg04 -ctgA example match 8545 8783 . - . Name=seg04 -ctgA example match 8869 8935 . - . Name=seg04 -ctgA example match 9404 9825 . - . Name=seg04 -ctgA example match 26503 26799 . - . Name=seg05 -ctgA example match 27172 27185 . - . Name=seg05 -ctgA example match 27448 27860 . - . Name=seg05 -ctgA example match 27887 28076 . - . Name=seg05 -ctgA example match 28225 28316 . - . Name=seg05 -ctgA example match 28777 29058 . - . Name=seg05 -ctgA example match 29513 29647 . - . Name=seg05 -ctgA example match 30108 30216 . - . Name=seg05 -ctgA example match 30465 30798 . - . Name=seg05 -ctgA example match 31232 31236 . - . Name=seg05 -ctgA example match 31421 31817 . - . Name=seg05 -ctgA example match 32010 32057 . - . Name=seg05 -ctgA example match 32208 32680 . - . Name=seg05 -ctgA example match 33053 33325 . - . Name=seg05 -ctgA example match 33438 33868 . - . Name=seg05 -ctgA example match 34244 34313 . - . Name=seg05 -ctgA example match 34605 34983 . - . Name=seg05 -ctgA example match 35333 35507 . - . Name=seg05 -ctgA example match 35642 35904 . - . Name=seg05 -ctgA example match 19249 19559 . + . Name=seg06 -ctgA example match 19975 20260 . + . Name=seg06 -ctgA example match 20379 20491 . + . Name=seg06 -ctgA example match 20533 21005 . + . Name=seg06 -ctgA example match 21122 21331 . + . Name=seg06 -ctgA example match 21682 22176 . + . Name=seg06 -ctgA example match 22374 22570 . + . Name=seg06 -ctgA example match 23025 23427 . + . Name=seg06 -ctgA example match 44191 44514 . - . Name=seg07 -ctgA example match 44552 45043 . - . Name=seg07 -ctgA example match 45373 45600 . - . Name=seg07 -ctgA example match 45897 46315 . - . Name=seg07 -ctgA example match 46491 46890 . - . Name=seg07 -ctgA example match 47126 47297 . - . Name=seg07 -ctgA example match 47735 47983 . - . Name=seg07 -ctgA example match 48447 48709 . - . Name=seg07 -ctgA example match 48931 49186 . - . Name=seg07 -ctgA example match 49472 49699 . - . Name=seg07 -ctgA example match 49957 50000 . - . Name=seg07 -ctgA example match 18509 18985 . + . Name=seg08 -ctgA example match 18989 19388 . + . Name=seg08 -ctgA example match 19496 19962 . + . Name=seg08 -ctgA example match 20093 20580 . + . Name=seg08 -ctgA example match 20970 21052 . + . Name=seg08 -ctgA example match 21270 21277 . + . Name=seg08 -ctgA example match 21685 22168 . + . Name=seg08 -ctgA example match 22564 22869 . + . Name=seg08 -ctgA example match 22958 23298 . + . Name=seg08 -ctgA example match 23412 23469 . + . Name=seg08 -ctgA example match 23932 23932 . + . Name=seg08 -ctgA example match 24328 24787 . + . Name=seg08 -ctgA example match 25228 25367 . + . Name=seg08 -ctgA example match 36616 37057 . - . Name=seg09 -ctgA example match 37208 37227 . - . Name=seg09 -ctgA example match 29771 29942 . + . Name=seg10 -ctgA example match 30042 30340 . + . Name=seg10 -ctgA example match 30810 31307 . + . Name=seg10 -ctgA example match 31761 31984 . + . Name=seg10 -ctgA example match 32374 32937 . + . Name=seg10 -ctgA example match 24228 24510 . + . Name=seg11 -ctgA example match 24868 25012 . + . Name=seg11 -ctgA example match 25212 25426 . + . Name=seg11 -ctgA example match 25794 25874 . + . Name=seg11 -ctgA example match 26075 26519 . + . Name=seg11 -ctgA example match 26930 26940 . + . Name=seg11 -ctgA example match 26975 27063 . + . Name=seg11 -ctgA example match 27415 27799 . + . Name=seg11 -ctgA example match 27880 27943 . + . Name=seg11 -ctgA example match 28225 28346 . + . Name=seg11 -ctgA example match 28375 28570 . + . Name=seg11 -ctgA example match 28758 29041 . + . Name=seg11 -ctgA example match 29101 29302 . + . Name=seg11 -ctgA example match 29604 29702 . + . Name=seg11 -ctgA example match 29867 29885 . + . Name=seg11 -ctgA example match 30241 30246 . + . Name=seg11 -ctgA example match 30575 30738 . + . Name=seg11 -ctgA example match 12531 12895 . + . Name=seg12 -ctgA example match 13122 13449 . + . Name=seg12 -ctgA example match 13452 13745 . + . Name=seg12 -ctgA example match 13908 13965 . + . Name=seg12 -ctgA example match 13998 14488 . + . Name=seg12 -ctgA example match 14564 14899 . + . Name=seg12 -ctgA example match 15185 15276 . + . Name=seg12 -ctgA example match 15639 15736 . + . Name=seg12 -ctgA example match 15745 15870 . + . Name=seg12 -ctgA example match 49406 49476 . + . Name=seg13 -ctgA example match 49762 50000 . + . Name=seg13 -ctgA example match 41137 41318 . - . Name=seg14 -ctgA example match 41754 41948 . - . Name=seg14 -ctgA example match 42057 42474 . - . Name=seg14 -ctgA example match 42890 43270 . - . Name=seg14 -ctgA example match 43395 43811 . - . Name=seg14 -ctgA example match 44065 44556 . - . Name=seg14 -ctgA example match 44763 45030 . - . Name=seg14 -ctgA example match 45231 45488 . - . Name=seg14 -ctgA example match 45790 46022 . - . Name=seg14 -ctgA example match 46092 46318 . - . Name=seg14 -ctgA example match 46816 46992 . - . Name=seg14 -ctgA example match 47449 47829 . - . Name=seg14 -ctgA example match 39265 39361 . - . Name=seg15 -ctgA example match 39753 40034 . - . Name=seg15 -ctgA example match 40515 40954 . - . Name=seg15 -ctgA example match 41252 41365 . - . Name=seg15 -ctgA example match 41492 41504 . - . Name=seg15 -ctgA example match 41941 42377 . - . Name=seg15 -ctgA example match 42748 42954 . - . Name=seg15 -ctgA example match 43401 43897 . - . Name=seg15 -ctgA example match 44043 44113 . - . Name=seg15 -ctgA example match 44399 44888 . - . Name=seg15 -ctgA example match 45281 45375 . - . Name=seg15 -ctgA example match 45711 46041 . - . Name=seg15 -ctgA example match 46425 46564 . - . Name=seg15 -ctgA example match 46738 47087 . - . Name=seg15 -ctgA example match 47329 47595 . - . Name=seg15 -ctgA example match 47858 47979 . - . Name=seg15 -ctgA example match 48169 48453 . - . Name=seg15 +ctgA example match 32329 32359 . + 825 Name=seg01 +ctgA example match 26122 26126 . + 185 Name=seg02 +ctgA example match 26497 26869 . + 502 Name=seg02 +ctgA example match 27201 27325 . + 442 Name=seg02 +ctgA example match 27372 27433 . + 970 Name=seg02 +ctgA example match 27565 27565 . + 519 Name=seg02 +ctgA example match 27813 28091 . + 592 Name=seg02 +ctgA example match 28093 28201 . + 475 Name=seg02 +ctgA example match 28329 28377 . + 17 Name=seg02 +ctgA example match 28829 29194 . + 276 Name=seg02 +ctgA example match 29517 29702 . + 492 Name=seg02 +ctgA example match 29713 30061 . + 465 Name=seg02 +ctgA example match 30329 30774 . + 525 Name=seg02 +ctgA example match 30808 31306 . + 619 Name=seg02 +ctgA example match 31516 31729 . + 248 Name=seg02 +ctgA example match 31753 32154 . + 613 Name=seg02 +ctgA example match 32595 32696 . + 701 Name=seg02 +ctgA example match 32892 32901 . + 724 Name=seg02 +ctgA example match 33127 33388 . + 977 Name=seg02 +ctgA example match 33439 33443 . + 502 Name=seg02 +ctgA example match 33759 34209 . + 415 Name=seg02 +ctgA example match 34401 34466 . + 746 Name=seg02 +ctgA example match 6885 7241 . - 40 Name=seg03 +ctgA example match 7410 7737 . - 830 Name=seg03 +ctgA example match 8055 8080 . - 943 Name=seg03 +ctgA example match 8306 8999 . - 658 Name=seg03 +ctgA example match 5233 5302 . - 467 Name=seg04 +ctgA example match 5800 6101 . - 711 Name=seg04 +ctgA example match 6442 6854 . - 533 Name=seg04 +ctgA example match 7106 7211 . - 646 Name=seg04 +ctgA example match 7695 8177 . - 479 Name=seg04 +ctgA example match 8545 8783 . - 568 Name=seg04 +ctgA example match 8869 8935 . - 62 Name=seg04 +ctgA example match 9404 9825 . - 191 Name=seg04 +ctgA example match 26503 26799 . - 645 Name=seg05 +ctgA example match 27172 27185 . - 774 Name=seg05 +ctgA example match 27448 27860 . - 643 Name=seg05 +ctgA example match 27887 28076 . - 361 Name=seg05 +ctgA example match 28225 28316 . - 444 Name=seg05 +ctgA example match 28777 29058 . - 109 Name=seg05 +ctgA example match 29513 29647 . - 67 Name=seg05 +ctgA example match 30108 30216 . - 964 Name=seg05 +ctgA example match 30465 30798 . - 563 Name=seg05 +ctgA example match 31232 31236 . - 313 Name=seg05 +ctgA example match 31421 31817 . - 530 Name=seg05 +ctgA example match 32010 32057 . - 788 Name=seg05 +ctgA example match 32208 32680 . - 441 Name=seg05 +ctgA example match 33053 33325 . - 152 Name=seg05 +ctgA example match 33438 33868 . - 226 Name=seg05 +ctgA example match 34244 34313 . - 838 Name=seg05 +ctgA example match 34605 34983 . - 529 Name=seg05 +ctgA example match 35333 35507 . - 822 Name=seg05 +ctgA example match 35642 35904 . - 107 Name=seg05 +ctgA example match 19249 19559 . + 404 Name=seg06 +ctgA example match 19975 20260 . + 882 Name=seg06 +ctgA example match 20379 20491 . + 16 Name=seg06 +ctgA example match 20533 21005 . + 645 Name=seg06 +ctgA example match 21122 21331 . + 237 Name=seg06 +ctgA example match 21682 22176 . + 36 Name=seg06 +ctgA example match 22374 22570 . + 893 Name=seg06 +ctgA example match 23025 23427 . + 169 Name=seg06 +ctgA example match 44191 44514 . - 295 Name=seg07 +ctgA example match 44552 45043 . - 645 Name=seg07 +ctgA example match 45373 45600 . - 683 Name=seg07 +ctgA example match 45897 46315 . - 580 Name=seg07 +ctgA example match 46491 46890 . - 291 Name=seg07 +ctgA example match 47126 47297 . - 880 Name=seg07 +ctgA example match 47735 47983 . - 587 Name=seg07 +ctgA example match 48447 48709 . - 159 Name=seg07 +ctgA example match 48931 49186 . - 496 Name=seg07 +ctgA example match 49472 49699 . - 921 Name=seg07 +ctgA example match 49957 50000 . - 226 Name=seg07 +ctgA example match 18509 18985 . + 915 Name=seg08 +ctgA example match 18989 19388 . + 791 Name=seg08 +ctgA example match 19496 19962 . + 600 Name=seg08 +ctgA example match 20093 20580 . + 140 Name=seg08 +ctgA example match 20970 21052 . + 460 Name=seg08 +ctgA example match 21270 21277 . + 228 Name=seg08 +ctgA example match 21685 22168 . + 373 Name=seg08 +ctgA example match 22564 22869 . + 570 Name=seg08 +ctgA example match 22958 23298 . + 831 Name=seg08 +ctgA example match 23412 23469 . + 811 Name=seg08 +ctgA example match 23932 23932 . + 22 Name=seg08 +ctgA example match 24328 24787 . + 894 Name=seg08 +ctgA example match 25228 25367 . + 463 Name=seg08 +ctgA example match 36616 37057 . - 736 Name=seg09 +ctgA example match 37208 37227 . - 409 Name=seg09 +ctgA example match 29771 29942 . + 402 Name=seg10 +ctgA example match 30042 30340 . + 513 Name=seg10 +ctgA example match 30810 31307 . + 22 Name=seg10 +ctgA example match 31761 31984 . + 228 Name=seg10 +ctgA example match 32374 32937 . + 752 Name=seg10 +ctgA example match 24228 24510 . + 35 Name=seg11 +ctgA example match 24868 25012 . + 276 Name=seg11 +ctgA example match 25212 25426 . + 709 Name=seg11 +ctgA example match 25794 25874 . + 666 Name=seg11 +ctgA example match 26075 26519 . + 604 Name=seg11 +ctgA example match 26930 26940 . + 31 Name=seg11 +ctgA example match 26975 27063 . + 764 Name=seg11 +ctgA example match 27415 27799 . + 973 Name=seg11 +ctgA example match 27880 27943 . + 823 Name=seg11 +ctgA example match 28225 28346 . + 931 Name=seg11 +ctgA example match 28375 28570 . + 697 Name=seg11 +ctgA example match 28758 29041 . + 241 Name=seg11 +ctgA example match 29101 29302 . + 343 Name=seg11 +ctgA example match 29604 29702 . + 771 Name=seg11 +ctgA example match 29867 29885 . + 147 Name=seg11 +ctgA example match 30241 30246 . + 949 Name=seg11 +ctgA example match 30575 30738 . + 928 Name=seg11 +ctgA example match 12531 12895 . + 693 Name=seg12 +ctgA example match 13122 13449 . + 750 Name=seg12 +ctgA example match 13452 13745 . + 502 Name=seg12 +ctgA example match 13908 13965 . + 177 Name=seg12 +ctgA example match 13998 14488 . + 605 Name=seg12 +ctgA example match 14564 14899 . + 939 Name=seg12 +ctgA example match 15185 15276 . + 249 Name=seg12 +ctgA example match 15639 15736 . + 597 Name=seg12 +ctgA example match 15745 15870 . + 364 Name=seg12 +ctgA example match 49406 49476 . + 706 Name=seg13 +ctgA example match 49762 50000 . + 605 Name=seg13 +ctgA example match 41137 41318 . - 729 Name=seg14 +ctgA example match 41754 41948 . - 21 Name=seg14 +ctgA example match 42057 42474 . - 63 Name=seg14 +ctgA example match 42890 43270 . - 356 Name=seg14 +ctgA example match 43395 43811 . - 70 Name=seg14 +ctgA example match 44065 44556 . - 430 Name=seg14 +ctgA example match 44763 45030 . - 730 Name=seg14 +ctgA example match 45231 45488 . - 531 Name=seg14 +ctgA example match 45790 46022 . - 247 Name=seg14 +ctgA example match 46092 46318 . - 552 Name=seg14 +ctgA example match 46816 46992 . - 547 Name=seg14 +ctgA example match 47449 47829 . - 879 Name=seg14 +ctgA example match 39265 39361 . - 750 Name=seg15 +ctgA example match 39753 40034 . - 875 Name=seg15 +ctgA example match 40515 40954 . - 135 Name=seg15 +ctgA example match 41252 41365 . - 534 Name=seg15 +ctgA example match 41492 41504 . - 653 Name=seg15 +ctgA example match 41941 42377 . - 374 Name=seg15 +ctgA example match 42748 42954 . - 847 Name=seg15 +ctgA example match 43401 43897 . - 15 Name=seg15 +ctgA example match 44043 44113 . - 905 Name=seg15 +ctgA example match 44399 44888 . - 868 Name=seg15 +ctgA example match 45281 45375 . - 462 Name=seg15 +ctgA example match 45711 46041 . - 262 Name=seg15 +ctgA example match 46425 46564 . - 823 Name=seg15 +ctgA example match 46738 47087 . - 7 Name=seg15 +ctgA example match 47329 47595 . - 928 Name=seg15 +ctgA example match 47858 47979 . - 64 Name=seg15 +ctgA example match 48169 48453 . - 305 Name=seg15 # single exon gene - one CDS only ctgA bare_predicted CDS 10000 11500 . + 0 Name=Apple1;Note=CDS with no parent diff -r eb3af6e9f633 -r e6440d0201f7 test-data/1/links3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1/links3.txt Fri Jun 30 06:48:38 2017 -0400 @@ -0,0 +1,50 @@ +ctgA 31880 35657 ctgB 2829 2901 value=517 +ctgA 7012 8404 ctgB 15 74 value=261 +ctgA 7702 7901 ctgB 382 442 value=441 +ctgA 22754 27176 ctgB 5459 5461 value=88 +ctgA 24212 24536 ctgB 2694 2700 value=622 +ctgA 31658 36109 ctgB 2498 2515 value=654 +ctgA 39454 42379 ctgB 1913 1922 value=423 +ctgA 4392 5685 ctgB 4311 4321 value=132 +ctgA 38384 40909 ctgB 63 142 value=692 +ctgA 5846 6169 ctgB 5866 5886 value=985 +ctgA 28176 31996 ctgB 798 821 value=788 +ctgA 3595 4052 ctgB 1309 1340 value=351 +ctgA 21222 24119 ctgB 3285 3363 value=474 +ctgA 1814 3350 ctgB 5825 5875 value=888 +ctgA 39805 40260 ctgB 4755 4807 value=709 +ctgA 38751 39742 ctgB 2624 2652 value=679 +ctgA 29916 32332 ctgB 3538 3576 value=473 +ctgA 11546 15551 ctgB 2991 3002 value=89 +ctgA 38404 40067 ctgB 5748 5769 value=811 +ctgA 7309 11935 ctgB 941 992 value=443 +ctgA 5176 9384 ctgB 5096 5111 value=364 +ctgA 36748 38074 ctgB 4238 4275 value=521 +ctgA 33782 38545 ctgB 4441 4516 value=372 +ctgA 29704 32992 ctgB 466 498 value=279 +ctgA 8676 8713 ctgB 5570 5612 value=239 +ctgA 26820 27834 ctgB 1949 1982 value=327 +ctgA 4809 6940 ctgB 5379 5442 value=426 +ctgA 43603 44903 ctgB 1939 1982 value=357 +ctgA 39061 43267 ctgB 5508 5525 value=240 +ctgA 35865 37777 ctgB 3475 3529 value=193 +ctgA 44675 49525 ctgB 5791 5829 value=237 +ctgA 30278 33936 ctgB 4047 4059 value=94 +ctgA 41726 43137 ctgB 4290 4291 value=445 +ctgA 1433 4466 ctgB 751 825 value=155 +ctgA 16012 20896 ctgB 1790 1815 value=264 +ctgA 14338 17126 ctgB 4623 4649 value=124 +ctgA 39161 40286 ctgB 3648 3694 value=580 +ctgA 37030 39122 ctgB 2151 2193 value=163 +ctgA 15200 15631 ctgB 4241 4299 value=334 +ctgA 19061 19621 ctgB 2299 2336 value=259 +ctgA 19623 24108 ctgB 2132 2152 value=422 +ctgA 25083 29108 ctgB 268 279 value=228 +ctgA 1270 6208 ctgB 106 179 value=964 +ctgA 416 2394 ctgB 901 943 value=58 +ctgA 37007 37698 ctgB 1186 1229 value=543 +ctgA 9921 14264 ctgB 594 643 value=949 +ctgA 33601 34598 ctgB 3515 3570 value=2 +ctgA 14677 16948 ctgB 4542 4604 value=352 +ctgA 11327 13114 ctgB 4965 4988 value=903 +ctgA 13680 16272 ctgB 32 50 value=575 diff -r eb3af6e9f633 -r e6440d0201f7 tmp.tar.gz Binary file tmp.tar.gz has changed diff -r eb3af6e9f633 -r e6440d0201f7 unified-tiles.py --- a/unified-tiles.py Sat Jun 10 16:21:01 2017 -0400 +++ b/unified-tiles.py Fri Jun 30 06:48:38 2017 -0400 @@ -62,6 +62,7 @@ lineExtra = [ 'strand=%s' % item[4], 'score=%s' % item[5], + 'value=%s' % item[5], ] if item[3] is not None: lineExtra.append('id=%s' % item[3]) diff -r eb3af6e9f633 -r e6440d0201f7 wiggle.pyc Binary file wiggle.pyc has changed