Mercurial > repos > eric-rasche > circos
changeset 9:e6440d0201f7 draft default tip
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7e335df423e3e06da3d33a5378a336a149e6cc6c
| author | eric-rasche |
|---|---|
| date | Fri, 30 Jun 2017 06:48:38 -0400 |
| parents | eb3af6e9f633 |
| children | |
| files | circos/circos.png circos/circos.svg circos/conf/2d.conf circos/conf/circos.conf circos/conf/galaxy_test_case.xml circos/conf/highlight.conf circos/conf/ideogram.conf circos/conf/karyotype.txt circos/conf/links.conf circos/conf/plot_highlight.conf circos/conf/ticks.conf circos/data/data-0.txt circos/data/data-1.txt generate_links.py macros.xml macros_conffiles.xml test-data/1/1.gff3 test-data/1/links3.txt tmp.tar.gz unified-tiles.py wiggle.pyc |
| diffstat | 21 files changed, 1440 insertions(+), 171 deletions(-) [+] |
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height="10" patternTransform="rotate(0 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:5" /></pattern> +<pattern id="checker" width="10" height="10" patternTransform="rotate(45 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:5" /><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:4" /></pattern> +<pattern id="checker" width="10" height="10" patternTransform="rotate(45 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:2" /><line x1="0" y1="0" x2="0" y2="10" style="stroke:black;stroke-width:2" /></pattern> +<pattern id="hline-sparse" width="10" height="10" patternTransform="rotate(0 0 0)" patternUnits="userSpaceOnUse"><line x1="0" y1="0" x2="10" y2="0" style="stroke:black;stroke-width:2" /></pattern> +</defs> +</svg>
--- /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 @@ +<plot> + + 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 + + + <rules> + <rule> + condition = 1 + color = eval(sprintf("brbg-15-div-%d", remap_int(var(value), 0.0, 12000.0, 1, 15))) + </rule> + </rules> + + <axes> + </axes> + <backgrounds> + </backgrounds> +</plot> +
--- /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 @@ + +<<include colors_fonts_patterns.conf>> +<<include housekeeping.conf>> +karyotype = karyotype.txt + +<image> + <<include etc/image.conf>> +</image> + +<<include ticks.conf>> +<<include ideogram.conf>> +<plots> + <<include 2d.conf>> + <<include plot_highlight.conf>> +</plots> +<links> + <<include links.conf>> +</links> + +<<include highlight.conf>> + \ No newline at end of file
--- /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 @@ + +<!-- +mkdir -p test-data/my-test-case/; + cp /tmp/tmprZFxwp/files/000/dataset_5.dat test-data/my-test-case/input.fa; + + +cp /tmp/tmprZFxwp/files/000/dataset_8.dat test-data/my-test-case/0-0.wig; +cp /tmp/tmprZFxwp/files/000/dataset_7.dat test-data/my-test-case/1.gff3; +cp "/tmp/tmprZFxwp/files/000/dataset_40.dat" test-data/my-test-case/output.png; +cp "/tmp/tmprZFxwp/files/000/dataset_41.dat" test-data/my-test-case/output.svg; +--> +<test> + <param name="reference_genome|reference_genome_source" value="history"/> + <param name="reference_genome|genome_fasta" value="my-test-case/input.fa" /> + <!-- ideograms --> + <param name="ideogram|spacing" value="0.005" /> + <param name="ideogram|radius" value="0.9" /> + <param name="ideogram|thickness" value="10.0" /> + <param name="ideogram|ideogram_labels|show_label" value="yes" /> + <param name="ideogram|ideogram_labels|parallel" value="yes" /> + <!-- Ticks --> + <param name="ticks|show_ticks" value="yes" /> + <param name="ticks|radius" value="1.0" /> + <param name="ticks|color" value="#000000" /> + <param name="ticks|multiplier" value="0.001" /> + <param name="ticks|tick_group_0|tickspacing" value="5000.0" /> + <param name="ticks|tick_group_0|size" value="10.0" /> + <param name="ticks|tick_group_0|show_tick_labels" value="yes" /> + <param name="ticks|tick_group_0|label_size" value="20.0" /> + <param name="ticks|tick_group_0|label_offset" value="10.0" /> + <param name="ticks|tick_group_0|label_format" value="%d" /> + <param name="ticks|tick_group_1|tickspacing" value="1000.0" /> + <param name="ticks|tick_group_1|size" value="5.0" /> + <param name="ticks|tick_group_1|show_tick_labels" value="no" /> + <param name="ticks|tick_group_1|label_size" value="20.0" /> + <param name="ticks|tick_group_1|label_offset" value="10.0" /> + <param name="ticks|tick_group_1|label_format" value="%d" /> + <!-- Data --> + <param name="sec_tdd|data_0|r0" value="0.95" /> + <param name="sec_tdd|data_0|r1" value="0.99" /> + <param name="sec_tdd|data_0|orientation" value="out" /> + <param name="sec_tdd|data_0|plot_format|plot_format_select" value="histogram" /> + <!-- Note, please double check your files --> + <param name="sec_tdd|data_0|plot_format|data_source" value="my-test-case/0-0.wig" /> + <param name="sec_tdd|data_0|plot_format|format_specific|fill_color" value="brbg-15-div" /> + <param name="sec_tdd|data_0|plot_format|format_specific|extend_bins" value="yes" /> + + <param name="sec_tdd|data_1|r0" value="0.8" /> + <param name="sec_tdd|data_1|r1" value="0.95" /> + <param name="sec_tdd|data_1|orientation" value="out" /> + <param name="sec_tdd|data_1|plot_format|plot_format_select" value="tile" /> + <!-- Note, please double check your files --> + <param name="sec_tdd|data_1|plot_format|data_source" value="my-test-case/1.gff3" /> + <param name="sec_tdd|data_1|plot_format|format_specific|fill_color" value="oranges-13-seq" /> + <param name="sec_tdd|data_1|plot_format|format_specific|color" value="#000000" /> + <param name="sec_tdd|data_1|plot_format|format_specific|stroke_thickness" value="1" /> + <param name="sec_tdd|data_1|plot_format|format_specific|layers" value="20" /> + <param name="sec_tdd|data_1|plot_format|format_specific|thickness" value="8.0" /> + <param name="sec_tdd|data_1|plot_format|format_specific|padding" value="2.0" /> + <param name="sec_tdd|data_1|plot_format|format_specific|overflow|overflow_behavior" value="grow" /> + <param name="sec_tdd|data_1|plot_format|format_specific|overflow|layer_overflow_color" value="#000000" /> + + + + <!-- Outputs --> + <output name="output_png" file="my-test-case/output.png" /> + <output name="output_svg" file="my-test-case/output.svg" /> +</test> + \ No newline at end of file
--- /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
--- /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 @@ + + +<ideogram> + + <spacing> + default = 0.005r + </spacing> + + # 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 + +</ideogram>
--- /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
--- /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
--- /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
--- /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 + + + +<ticks> + radius = 1.0r + color = 0, 0, 0 + + thickness = 2p + multiplier = 0.001 + + <tick> + spacing = 5000.0 + size = 10.0p + show_label = yes + label_size = 20.0p + label_offset = 10.0p + format = %d kb + </tick> + <tick> + spacing = 1000.0 + size = 5.0p + show_label = no + label_size = 20.0p + label_offset = 10.0p + format = %d kb + </tick> +</ticks> + + \ No newline at end of file
--- /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 1319 -0.91289603861164 +ctgA 1401 1419 -0.993901956906654 +ctgA 1501 1519 -0.801224790676895 +ctgA 1601 1619 -0.387920558984219 +ctgA 1701 1719 0.132202352755937 +ctgA 1801 1819 0.615921726468774 +ctgA 1901 1919 0.930039504416137 +ctgA 2001 2019 0.988059506793465 +ctgA 2101 2119 0.774005214886395 +ctgA 2201 2219 0.34681910129778 +ctgA 2301 2319 -0.175867902248536 +ctgA 2401 2419 -0.650127523574896 +ctgA 2501 2519 -0.945366563696042 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--- /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 +ctgA 1049 3202 strand=1,score=0.0,value=0.0,id=Match1 +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 +ctgA 1658 1984 strand=1,score=1110,value=1110,id=f07 +ctgA 1799 2900 strand=-1,score=0.0,value=0.0,id=Protein:HGB +ctgA 3013 6130 strand=1,score=999,value=999,id=f06 +ctgA 4714 5968 strand=-1,score=444,value=444,id=f05 +ctgA 5232 5302 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22957 23298 strand=1,score=0.0,value=0.0,id=seg08 +ctgA 23024 23427 strand=1,score=0.0,value=0.0,id=seg06 +ctgA 23071 23185 strand=1,score=850,value=850,id=f14 +ctgA 23411 23469 strand=1,score=0.0,value=0.0,id=seg08 +ctgA 23931 23932 strand=1,score=0.0,value=0.0,id=seg08 +ctgA 24227 24510 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 24327 24787 strand=1,score=0.0,value=0.0,id=seg08 +ctgA 24561 28338 strand=1,score=208,value=208,id=f02 +ctgA 24867 25012 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 25211 25426 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 25227 25367 strand=1,score=0.0,value=0.0,id=seg08 +ctgA 25793 25874 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 26074 26519 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 26121 26126 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 26496 26869 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 26502 26799 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 26929 26940 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 26974 27063 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 27171 27185 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 27200 27325 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 27371 27433 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 27414 27799 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 27447 27860 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 27564 27565 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 27812 28091 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 27879 27943 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 27886 28076 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 28092 28201 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 28224 28316 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 28224 28346 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 28328 28377 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 28331 30033 strand=-1,score=0.0,value=0.0,id=m02 +ctgA 28341 28447 strand=-1,score=0.0,value=0.0,id=m10 +ctgA 28374 28570 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 28757 29041 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 28776 29058 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 28828 29194 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 29100 29302 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 29512 29647 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 29516 29702 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 29603 29702 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 29712 30061 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 29770 29942 strand=1,score=0.0,value=0.0,id=seg10 +ctgA 29866 29885 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 30041 30340 strand=1,score=0.0,value=0.0,id=seg10 +ctgA 30107 30216 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 30240 30246 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 30328 30774 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 30464 30798 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 30574 30738 strand=1,score=0.0,value=0.0,id=seg11 +ctgA 30577 31748 strand=1,score=0.0,value=0.0,id=m06 +ctgA 30807 31306 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 30809 31307 strand=1,score=0.0,value=0.0,id=seg10 +ctgA 31231 31236 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 31420 31817 strand=-1,score=0.0,value=0.0,id=seg05 +ctgA 31515 31729 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 31752 32154 strand=1,score=0.0,value=0.0,id=seg02 +ctgA 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
--- /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), + ])))
--- 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 @@ <param name="action_value" type="integer" value="1" label="Thickness"/> </when> <when value="z"> - <param name="action_value" type="float" value="1" label="Z-depth" help="Datasets with a higher z-depth value are drawn on top of datasets with lower z value"/> + <conditional name="dynamic"> + <param name="dynamic_select" type="select" label="Static or Dynamic Z-Depth"> + <option value="static">Static</option> + <option value="dynamic">Dynamic (based on value)</option> + </param> + <when value="static"> + <param name="action_value" type="float" value="1" label="Z-depth" help="Datasets with a higher z-depth value are drawn on top of datasets with lower z value"/> + </when> + <when value="dynamic"> + <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> + <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/> + <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Z-Depth Mapping" /> + </when> + </conditional> </when> </conditional> </repeat>
--- 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
--- 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
--- /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