# 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 @@
+
+
+
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)))
+
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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 @@
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\ 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 @@
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+ctgA 48101 48119 0.993427755984289
+ctgA 48201 48219 0.914610560427116
+ctgA 48301 48319 0.583944138115545
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+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
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+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 1000 strand=None,score=0.987,value=0.987,id=FakeSNP1
+ctgA 999 20000 strand=None,score=0.0,value=0.0,id=b101.2
+ctgA 1049 9000 strand=1,score=0.0,value=0.0,id=EDEN
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+ctgA 1049 7300 strand=1,score=0.0,value=0.0,id=Match3
+ctgA 1099 2000 strand=1,score=0.0,value=0.0,id=Gene:hga
+ctgA 1149 7200 strand=1,score=0.0,value=0.0,id=Match5
+ctgA 1199 1900 strand=1,score=0.0,value=0.0,id=Protein:HGA
+ctgA 1599 3000 strand=-1,score=0.0,value=0.0,id=Gene:hgb
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+ctgA 1799 2900 strand=-1,score=0.0,value=0.0,id=Protein:HGB
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+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