| Previous changeset 5:a64dc31ab7f2 (2020-01-23) Next changeset 7:4b519282a05b (2020-05-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a" |
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modified:
circos.xml fasta-to-karyotype.py genome-lengths-to-karyotype.py macros.xml macros_conffiles.xml macros_tests.xml test-data/0/out.png test-data/0/out.svg test-data/1/out.png test-data/1/out.svg test-data/tiles/2.out tiles-from-gff3.py |
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added:
karyotype/karyotype.arabidopsis.tair10.txt karyotype/karyotype.chimp.pt4.txt karyotype/karyotype.drosophila.dm6.hires.txt karyotype/karyotype.drosophila.hires.dm3.txt karyotype/karyotype.human.hg16.txt karyotype/karyotype.human.hg17.txt karyotype/karyotype.human.hg18.txt karyotype/karyotype.human.hg19.txt karyotype/karyotype.human.hg38.txt karyotype/karyotype.mouse.mm10.txt karyotype/karyotype.mouse.mm9.txt karyotype/karyotype.oryzasativa.txt karyotype/karyotype.rat.rn4.txt karyotype/karyotype.sorghum.txt karyotype/karyotype.yeast.txt karyotype/karyotype.zeamays.txt stack-histogram.py stack-histogram.xml test-data/scatter/1.multi.out |
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| diff -r a64dc31ab7f2 -r 740057a5126d circos.xml --- a/circos.xml Thu Jan 23 07:27:22 2020 -0500 +++ b/circos.xml Fri May 01 07:28:50 2020 -0400 |
| [ |
| b'@@ -1,6 +1,11 @@\n <?xml version="1.0"?>\n <tool id="circos" name="Circos" version="@WRAPPER_VERSION@">\n <description>visualizes data in a circular layout</description>\n+ <xrefs>\n+ <xref type="bio.tools">galactic_circos</xref>\n+ <!--<xref type="bioconda">circos</xref>-->\n+ <!--<xref type="rrid">RRID:SCR_018207</xref>-->\n+ </xrefs>\n <macros>\n <import>macros.xml</import>\n <import>macros_conffiles.xml</import>\n@@ -8,7 +13,14 @@\n </macros>\n <expand macro="requirements"/>\n <version_command>circos --version</version_command>\n- <command detect_errors="exit_code"><![CDATA[\n+ <stdio>\n+ <!-- Anything other than zero is an error -->\n+ <exit_code range="1:"/>\n+ <exit_code range=":-1"/>\n+ <!-- In case the return code has not been set propery check stderr too -->\n+ <regex match="Circos::Error::fatal_error.* called at"/>\n+ </stdio>\n+ <command><![CDATA[\n ## Directory structure\n mkdir -p circos/conf/ circos/data/ &&\n \n@@ -29,7 +41,7 @@\n <(head -n 50 \'${reference_genome.ref.fasta_indexes.fields.len_path}\')\n #end if\n #end if\n- \'${ideogram.color}\'\n+ \'${reference_genome.ref.color}\'\n > circos/conf/karyotype.txt &&\n #else if $reference_genome.ref.ref_source == \'karyotype\':\n cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt &&\n@@ -38,23 +50,26 @@\n python\n \'$__tool_directory__/fasta-to-karyotype.py\'\n genomeref.fa\n- \'${ideogram.color}\'\n+ \'${reference_genome.ref.color}\'\n \n > circos/conf/karyotype.txt &&\n+#else if $reference_genome.ref.ref_source == \'preset\':\n+ cp \'$__tool_directory__/karyotype/\'${reference_genome.ref.preset_karyotype} circos/conf/karyotype.txt &&\n #end if\n \n touch circos/conf/karyotype-colors.conf &&\n-#if $ideogram.bands.bands:\n- #if $ideogram.bands.convert_bands:\n- python \'$__tool_directory__/process-cytogenetic-bands.py\'\n- \'${ideogram.bands.bands}\'\n- >> circos/conf/karyotype.txt\n- 2> circos/conf/karyotype-colors.conf &&\n- #else\n- cat \'${ideogram.bands.bands}\'\n- >> circos/conf/karyotype.txt &&\n- #end if\n-#end if\n+\n+## #if $ideogram.bands.bands:\n+## #if $ideogram.bands.convert_bands:\n+## python \'$__tool_directory__/process-cytogenetic-bands.py\'\n+## \'${ideogram.bands.bands}\'\n+## >> circos/conf/karyotype.txt\n+## 2> circos/conf/karyotype-colors.conf &&\n+## #else\n+## cat \'${ideogram.bands.bands}\'\n+## >> circos/conf/karyotype.txt &&\n+## #end if\n+## #end if\n \n #if $plot_options.colour_profile:\n #if str($plot_options.colour_profile) == \'cg\':\n@@ -66,15 +81,9 @@\n cp \'$ticks_conf\' circos/conf/ticks.conf &&\n cp \'$ideogram_conf\' circos/conf/ideogram.conf &&\n cp \'$data_conf\' circos/conf/data.conf &&\n-cp \'$highlight_conf\' circos/conf/highlight.conf &&\n cp \'$links_conf\' circos/conf/links.conf &&\n cp \'$test_case_conf\' circos/conf/galaxy_test_case.json &&\n \n-## Highlights\n-#for $hi, $data in enumerate($sec_highlight.data):\n-cp \'${data.data_source}\' circos/data/highlight-${hi}.txt &&\n-#end for\n-\n ## 2D Data Plots\n #for $hi, $data in enumerate($sec_tdd.data):\n cp \'${data.plot_format.data_source}\' circos/data/data-${hi}.txt &&\n@@ -99,16 +108,16 @@\n <expand macro="configfile_ideogram_conf" />\n <expand macro="configfile_data_conf" />\n <expand macro="configfile_links_conf" />\n- <expand macro="configfile_highlight_conf" />\n <expand macro="test_case" />\n </configfiles>\n <inputs>\n <section name="reference_genome" title="Karyotype" expanded="true">\n <conditional name="ref">\n <param name="ref_source" type="select" label="Reference Genome Source">\n- <option value="history" selected="True">FASTA File from History</option>\n+ <option value="preset" selected="True">Circos Presets</opt'..b'="spacing" type="text" value="5000" label="Tick Spacing" help="Number of bases (number + u syntax works)"/>\n+ <param name="spacing" type="float" min="0" label="Tick Spacing" value="1" help="in chromosome units" />\n <param name="size" type="float" value="10" label="Tick Size"/>\n <expand macro="circos_color"/>\n <conditional name="ticks">\n@@ -478,16 +604,11 @@\n \n </section>\n \n- <section name="sec_highlight" title="Highlights">\n- <repeat name="data" title="Highlight" help="Highlights can help highlight a specific region by placing a large coloured block under some interesting or important features that the audience\'s eyes should be drawn towards">\n- <param name="r1" type="float" value="0.89" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/>\n- <param name="r0" type="float" value="0.8" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/>\n- <param name="data_source" type="data" format="tabular,interval" label="Highlight Data Source" help="Columns must be (chrom, start, end)"/>\n- <expand macro="circos_color_alpha" label="Fill Color" name="fill_color" value="#000000"/>\n- <expand macro="stroke_opts"/>\n- <expand macro="zdepth"/>\n- <expand macro="rules" />\n- </repeat>\n+ <section name="limits" title="Limits">\n+ <param name="max_ticks" type="integer" min="200" value="5000" label="Maximum number of ticks to draw" help="These are advanced options, if you increase these due to a plotting failure it may result in a significantly longer plotting time. Beware!"/>\n+ <param name="max_ideograms" type="integer" min="200" value="200" label="Maximum number of ideograms to draw"/>\n+ <param name="max_links" type="integer" min="200" value="25000" label="Maximum number of links to draw"/>\n+ <param name="max_points_per_track" type="integer" min="200" value="25000" label="Maximum number of points per track"/>\n </section>\n \n <section name="outputs" title="Outputs">\n@@ -506,12 +627,25 @@\n <data name="output_tar" format="tar.gz" from_work_dir="circos.tar.gz" label="Circos Conf Files">\n <filter>outputs[\'tar\']</filter>\n </data>\n+ <data name="karyotype_txt" format="tabular" from_work_dir="circos/conf/karyotype.txt" label="Circos Karyotype">\n+ <filter>reference_genome[\'ref\'][\'ref_source\'] != \'karyotype\' and reference_genome[\'ref\'][\'ref_source\'] != \'preset\' </filter>\n+ </data>\n </outputs>\n <expand macro="test_cases" />\n <help><![CDATA[\n Circos\n ======\n \n+.. class:: infomark\n+\n+ Made a nice plot? Share it with us in the `training materials <https://github.com/galaxyproject/training-material/issues/1867>`__, we\'re looking for more cool plots with scientifically relevant stories to share with the students who want to learn how to use Circos.\n+\n+ Have a feature request? `Share it with us! <https://github.com/galaxyproject/training-material/issues/1867>`__\n+\n+.. class:: warningmark\n+\n+ No data or plot crashes? Check that your chromosome naming scheme matches between your Karyotype file and your datasets.\n+\n Circos is a software package for visualizing data and information. It visualizes data in a circular layout \xe2\x80\x94 this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive.\n \n Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure to tailor its focus points and detail to your audience.\n' |
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| diff -r a64dc31ab7f2 -r 740057a5126d fasta-to-karyotype.py --- a/fasta-to-karyotype.py Thu Jan 23 07:27:22 2020 -0500 +++ b/fasta-to-karyotype.py Fri May 01 07:28:50 2020 -0400 |
| [ |
| @@ -6,7 +6,7 @@ # Process fasta data, extracting only headers for idx, seq in enumerate(SeqIO.parse(sys.argv[1], "fasta")): sys.stdout.write( - "chr - {seq_id} {seq_id} 0 {length} {theme}-{color}\n".format( + "chr - {seq_id} {seq_id} 0 {length} {theme}-{color}\n".format( seq_id=seq.id, idx=idx, length=len(seq), |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d genome-lengths-to-karyotype.py --- a/genome-lengths-to-karyotype.py Thu Jan 23 07:27:22 2020 -0500 +++ b/genome-lengths-to-karyotype.py Fri May 01 07:28:50 2020 -0400 |
| [ |
| @@ -14,7 +14,7 @@ length = row[1] sys.stdout.write( - "chr - {seq_id} {seq_id} 0 {length} {theme}-{color}\n".format( + "chr - {seq_id} {seq_id} 0 {length} {theme}-{color}\n".format( seq_id=seq_id, idx=idx, length=length, |
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| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.arabidopsis.tair10.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.arabidopsis.tair10.txt Fri May 01 07:28:50 2020 -0400 |
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| @@ -0,0 +1,5 @@ +chr - chr1 chr1 0 30427617 chr1 +chr - chr2 chr2 0 19698289 chr2 +chr - chr3 chr3 0 23459830 chr3 +chr - chr4 chr4 0 18585056 chr4 +chr - chr5 chr5 0 26975502 chr5 |
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| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.chimp.pt4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.chimp.pt4.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| @@ -0,0 +1,122 @@ +chr - ptm m 0 16554 chrm +chr - ptX X 0 156848144 chrX +chr - ptY Y 0 26342871 chrY +chr - pt1 1 0 228333871 chr1 +chr - pt2a 2a 0 113622374 chr2a +chr - pt2b 2b 0 247518478 chr2b +chr - pt3 3 0 202329955 chr3 +chr - pt4 4 0 193495092 chr4 +chr - pt5 5 0 182651097 chr5 +chr - pt6 6 0 172623881 chr6 +chr - pt7 7 0 161824586 chr7 +chr - pt8 8 0 143986469 chr8 +chr - pt9 9 0 137840987 chr9 +chr - pt10 10 0 133524379 chr10 +chr - pt11 11 0 133121534 chr11 +chr - pt12 12 0 134246214 chr12 +chr - pt13 13 0 115123233 chr13 +chr - pt14 14 0 106544938 chr14 +chr - pt15 15 0 99548318 chr15 +chr - pt16 16 0 89983829 chr16 +chr - pt17 17 0 82630442 chr17 +chr - pt18 18 0 76611499 chr18 +chr - pt19 19 0 63644993 chr19 +chr - pt20 20 0 61729293 chr20 +chr - pt21 21 0 32799110 chr21 +chr - pt22 22 0 49737984 chr22 +band pt1 p p 0 113832284 gneg +band pt1 cen cen 113832284 114952284 acen +band pt1 cen cen 114952284 116072284 acen +band pt1 q q 116072284 228333871 gneg +band pt10 p p 0 39470229 gneg +band pt10 cen cen 39470229 40660229 acen +band pt10 cen cen 40660229 41850229 acen +band pt10 q q 41850229 133524379 gneg +band pt11 p p 0 50647596 gneg +band pt11 cen cen 50647596 52147596 acen +band pt11 cen cen 52147596 53647596 acen +band pt11 q q 53647596 133121534 gneg +band pt12 p p 0 52156499 gneg +band pt12 cen cen 52156499 52853999 acen +band pt12 cen cen 52853999 53551499 acen +band pt12 q q 53551499 134246214 gneg +band pt13 p p 0 16000000 gneg +band pt13 cen cen 16000000 16934000 acen +band pt13 cen cen 16934000 17868000 acen +band pt13 q q 17868000 115123233 gneg +band pt14 p p 0 15070000 gneg +band pt14 cen cen 15070000 16570000 acen +band pt14 cen cen 16570000 18070000 acen +band pt14 q q 18070000 106544938 gneg +band pt15 p p 0 15260000 gneg +band pt15 cen cen 15260000 16760000 acen +band pt15 cen cen 16760000 18260000 acen +band pt15 q q 18260000 99548318 gneg +band pt16 p p 0 42150972 gneg +band pt16 cen cen 42150972 43050972 acen +band pt16 cen cen 43050972 43950972 acen +band pt16 q q 43950972 89983829 gneg +band pt17 p p 0 33925834 gneg +band pt17 cen cen 33925834 33975834 acen +band pt17 cen cen 33975834 34025834 acen +band pt17 q q 34025834 82630442 gneg +band pt18 p p 0 82944 gneg +band pt18 cen cen 82944 764943 acen +band pt18 cen cen 764943 1446942 acen +band pt18 q q 1446942 76611499 gneg +band pt19 p p 0 26701495 gneg +band pt19 cen cen 26701495 28201495 acen +band pt19 cen cen 28201495 29701495 acen +band pt19 q q 29701495 63644993 gneg +band pt20 p p 0 26025681 gneg +band pt20 cen cen 26025681 26908511 acen +band pt20 cen cen 26908511 27791342 acen +band pt20 q q 27791342 61729293 gneg +band pt22 p p 0 11330000 gneg +band pt22 cen cen 11330000 12830000 acen +band pt22 cen cen 12830000 14330000 acen +band pt22 q q 14330000 49737984 gneg +band pt2a p p 0 91793653 gneg +band pt2a cen cen 91793653 93293653 acen +band pt2a cen cen 93293653 94793653 acen +band pt2a q q 94793653 113622374 gneg +band pt2b p p 0 132910908 gneg +band pt2b cen cen 132910908 134410908 acen +band pt2b cen cen 134410908 135910908 acen +band pt2b q q 135910908 247518478 gneg +band pt3 p p 0 92159186 gneg +band pt3 cen cen 92159186 93609186 acen +band pt3 cen cen 93609186 95059186 acen +band pt3 q q 95059186 202329955 gneg +band pt4 p p 0 78675172 gneg +band pt4 cen cen 78675172 80175172 acen +band pt4 cen cen 80175172 81675172 acen +band pt4 q q 81675172 193495092 gneg +band pt5 p p 0 65648281 gneg +band pt5 cen cen 65648281 67148281 acen +band pt5 cen cen 67148281 68648281 acen +band pt5 q q 68648281 182651097 gneg +band pt6 p p 0 59767044 gneg +band pt6 cen cen 59767044 61267044 acen +band pt6 cen cen 61267044 62767044 acen +band pt6 q q 62767044 172623881 gneg +band pt7 p p 0 58420265 gneg +band pt7 cen cen 58420265 59920265 acen +band pt7 cen cen 59920265 61420265 acen +band pt7 q q 61420265 161824586 gneg +band pt8 p p 0 40544052 gneg +band pt8 cen cen 40544052 42044052 acen +band pt8 cen cen 42044052 43544052 acen +band pt8 q q 43544052 143986469 gneg +band pt9 p p 0 45033823 gneg +band pt9 cen cen 45033823 46533823 acen +band pt9 cen cen 46533823 48033823 acen +band pt9 q q 48033823 137840987 gneg +band ptX p p 0 59308983 gneg +band ptX cen cen 59308983 60808983 acen +band ptX cen cen 60808983 62308983 acen +band ptX q q 62308983 156848144 gneg +band ptY p p 0 7528572 gneg +band ptY cen cen 7528572 7778572 acen +band ptY cen cen 7778572 8028573 acen +band ptY q q 8028573 26342871 gneg |
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| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.drosophila.dm6.hires.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.drosophila.dm6.hires.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,5048 @@\n+chr - M M 0 19524 set1-8-qual-1\n+chr - X X 0 23542271 set1-8-qual-2\n+chr - Y Y 0 3667352 set1-8-qual-3\n+chr - 2L 2L 0 23513712 set1-8-qual-4\n+chr - 2R 2R 0 25286936 set1-8-qual-5\n+chr - 3L 3L 0 28110227 set1-8-qual-6\n+chr - 3R 3R 0 32079331 set1-8-qual-7\n+chr - 4 4 0 1348131 set1-8-qual-8\n+band 2L 21b1 21b1 22221 98619 n/a\n+band 2L 21b2 21b2 98619 134010 n/a\n+band 2L 21b3 21b3 134010 161234 n/a\n+band 2L 21b4 21b4 161234 213130 n/a\n+band 2L 21b5 21b5 213130 256688 n/a\n+band 2L 21b6 21b6 256688 267408 n/a\n+band 2L 21b7 21b7 267408 294632 n/a\n+band 2L 21b8 21b8 294632 324485 n/a\n+band 2L 21c1 21c1 324485 390347 n/a\n+band 2L 21c2 21c2 390347 456209 n/a\n+band 2L 21c3 21c3 456209 456219 n/a\n+band 2L 21c4 21c4 456219 456229 n/a\n+band 2L 21c5 21c5 456229 456239 n/a\n+band 2L 21c6 21c6 456239 456249 n/a\n+band 2L 21c7 21c7 456249 458430 n/a\n+band 2L 21c8 21c8 458430 464653 n/a\n+band 2L 21d1 21d1 464653 482425 n/a\n+band 2L 21d2 21d2 482425 500197 n/a\n+band 2L 21d3 21d3 500197 510759 n/a\n+band 2L 21d4 21d4 510759 518418 n/a\n+band 2L 21e1 21e1 518418 533318 n/a\n+band 2L 21e2 21e2 533318 987803 n/a\n+band 2L 21e3 21e3 987803 1048634 n/a\n+band 2L 21e4 21e4 1048634 1086654 n/a\n+band 2L 21f1 21f1 1086654 1170535 n/a\n+band 2L 21f2 21f2 1170535 1224563 n/a\n+band 2L 21f3 21f3 1224563 1277401 n/a\n+band 2L 21f4 21f4 1277401 1326937 n/a\n+band 2L 22a1 22a1 1326937 1428804 n/a\n+band 2L 22a2 22a2 1428804 1530671 n/a\n+band 2L 22a3 22a3 1530671 1644731 n/a\n+band 2L 22a4 22a4 1644731 1644741 n/a\n+band 2L 22a5 22a5 1644741 1654988 n/a\n+band 2L 22a6 22a6 1654988 1667727 n/a\n+band 2L 22a7 22a7 1667727 1687818 n/a\n+band 2L 22a8 22a8 1687818 1698637 n/a\n+band 2L 22b1 22b1 1698637 1737370 n/a\n+band 2L 22b2 22b2 1737370 1802684 n/a\n+band 2L 22b3 22b3 1802684 1852361 n/a\n+band 2L 22b4 22b4 1852361 1902039 n/a\n+band 2L 22b5 22b5 1902039 1920281 n/a\n+band 2L 22b6 22b6 1920281 1954160 n/a\n+band 2L 22b7 22b7 1954160 1964421 n/a\n+band 2L 22b8 22b8 1964421 2014098 n/a\n+band 2L 22b9 22b9 2014098 2027808 n/a\n+band 2L 22c1 22c1 2027808 2061629 n/a\n+band 2L 22c2 22c2 2061629 2090832 n/a\n+band 2L 22c3 22c3 2090832 2132199 n/a\n+band 2L 22d1 22d1 2132199 2204105 n/a\n+band 2L 22d2 22d2 2204105 2204115 n/a\n+band 2L 22d3 22d3 2204115 2204125 n/a\n+band 2L 22d4 22d4 2204125 2234802 n/a\n+band 2L 22d5 22d5 2234802 2261169 n/a\n+band 2L 22d6 22d6 2261169 2298835 n/a\n+band 2L 22e1 22e1 2298835 2425019 n/a\n+band 2L 22e2 22e2 2425019 2425029 n/a\n+band 2L 22e3 22e3 2425029 2425039 n/a\n+band 2L 22e4 22e4 2425039 2425049 n/a\n+band 2L 22f1 22f1 2425049 2432797 n/a\n+band 2L 22f2 22f2 2432797 2458422 n/a\n+band 2L 22f3 22f3 2458422 2492448 n/a\n+band 2L 22f4 22f4 2492448 2564558 n/a\n+band 2L 23a1 23a1 2564558 2642867 n/a\n+band 2L 23a2 23a2 2642867 2721176 n/a\n+band 2L 23a3 23a3 2721176 2761795 n/a\n+band 2L 23a4 23a4 2761795 2762015 n/a\n+band 2L 23a5 23a5 2762015 2774487 n/a\n+band 2L 23a6 23a6 2774487 2786959 n/a\n+band 2L 23a7 23a7 2786959 2790737 n/a\n+band 2L 23b1 23b1 2790737 2809025 n/a\n+band 2L 23b2 23b2 2809025 2827313 n/a\n+band 2L 23b3 23b3 2827313 2839785 n/a\n+band 2L 23b4 23b4 2839785 2846501 n/a\n+band 2L 23b5 23b5 2846501 2856095 n/a\n+band 2L 23b6 23b6 2856095 2864302 n/a\n+band 2L 23b7 23b7 2864302 2870047 n/a\n+band 2L 23b8 23b8 2870047 2875792 n/a\n+band 2L 23c1 23c1 2875792 2888923 n/a\n+band 2L 23c2 23c2 2888923 2946983 n/a\n+band 2L 23c3 23c3 2946983 2972384 n/a\n+band 2L 23c4 23c4 2972384 3030443 n/a\n+band 2L 23c5 23c5 3030443 3066730 n/a\n+band 2L 23d1 23d1 3066730 3124790 n/a\n+band 2L 23d2 23d2 3124790 3145048 n/a\n+band 2L 23d3 23d3 3145048 3161507 n/a\n+band 2L 23d4 23d4 3161507 3186062 n/a\n+band 2L 23d5 23d5 3186062 3202164 n/a\n+band 2L 23d6 23d6 3202164 3218266 n/a\n+band 2L 23e1 23e1 3218266 3295327 n/a\n+band 2L 23e2 23e2 3295327 3298921 n/a\n+band 2L 23e3 23e3 3298921 3321924 n/a\n+band 2L 23e4 23e4 3321924 3344927 n/a\n+band 2L 23e5 23e5 3344927 3361029 n/a\n+band 2L 23e6 23e6 3361029 3370087 n/a\n+band 2L 23f1 23f1 3370087 3440247 n/a\n+band 2L 23f2 23f2 3440247 34438'..b'17f1 18858040 18869345 n/a\n+band X 17f2 17f2 18869345 18910754 n/a\n+band X 17f3 17f3 18910754 18936074 n/a\n+band X 18a1 18a1 18936074 19005026 n/a\n+band X 18a2 18a2 19005026 19073978 n/a\n+band X 18a3 18a3 19073978 19153782 n/a\n+band X 18a4 18a4 19153782 19174580 n/a\n+band X 18a5 18a5 19174580 19184006 n/a\n+band X 18a6 18a6 19184006 19190605 n/a\n+band X 18a7 18a7 19190605 19200032 n/a\n+band X 18b1 18b1 19200032 19220240 n/a\n+band X 18b2 18b2 19220240 19221713 n/a\n+band X 18b3 18b3 19221713 19231140 n/a\n+band X 18b4 18b4 19231140 19246222 n/a\n+band X 18b5 18b5 19246222 19249934 n/a\n+band X 18b6 18b6 19249934 19262189 n/a\n+band X 18b7 18b7 19262189 19274443 n/a\n+band X 18b8 18b8 19274443 19278155 n/a\n+band X 18b9 18b9 19278155 19284754 n/a\n+band X 18b10 18b10 19284754 19291353 n/a\n+band X 18b11 18b11 19291353 19295064 n/a\n+band X 18c1 18c1 19295064 19310147 n/a\n+band X 18c2 18c2 19310147 19342711 n/a\n+band X 18c3 18c3 19342711 19429338 n/a\n+band X 18c4 18c4 19429338 19432518 n/a\n+band X 18c5 18c5 19432518 19440532 n/a\n+band X 18c6 18c6 19440532 19466991 n/a\n+band X 18c7 18c7 19466991 19493450 n/a\n+band X 18c8 18c8 19493450 19555526 n/a\n+band X 18c9 18c9 19555526 19555536 n/a\n+band X 18d1 18d1 19555536 19570917 n/a\n+band X 18d2 18d2 19570917 19573161 n/a\n+band X 18d3 18d3 19573161 19616961 n/a\n+band X 18d4 18d4 19616961 19616971 n/a\n+band X 18d5 18d5 19616971 19616981 n/a\n+band X 18d6 18d6 19616981 19617184 n/a\n+band X 18d7 18d7 19617184 19625608 n/a\n+band X 18d8 18d8 19625608 19634033 n/a\n+band X 18d9 18d9 19634033 19634043 n/a\n+band X 18d10 18d10 19634043 19637550 n/a\n+band X 18d11 18d11 19637550 19644112 n/a\n+band X 18d12 18d12 19644112 19649160 n/a\n+band X 18d13 18d13 19649160 19676126 n/a\n+band X 18e1 18e1 19676126 19704229 n/a\n+band X 18e2 18e2 19704229 19706610 n/a\n+band X 18e3 18e3 19706610 19730045 n/a\n+band X 18e4 18e4 19730045 19732427 n/a\n+band X 18e5 18e5 19732427 19747669 n/a\n+band X 18f1 18f1 19747669 19781298 n/a\n+band X 18f2 18f2 19781298 19835953 n/a\n+band X 18f3 18f3 19835953 19851510 n/a\n+band X 18f4 18f4 19851510 19887071 n/a\n+band X 18f5 18f5 19887071 19887081 n/a\n+band X 19a1 19a1 19887081 19887091 n/a\n+band X 19a2 19a2 19887091 19922096 n/a\n+band X 19a3 19a3 19922096 19976855 n/a\n+band X 19a4 19a4 19976855 20031614 n/a\n+band X 19a5 19a5 20031614 20046908 n/a\n+band X 19a6 19a6 20046908 20068757 n/a\n+band X 19b1 19b1 20068757 20128705 n/a\n+band X 19b2 19b2 20128705 20132119 n/a\n+band X 19b3 19b3 20132119 20160523 n/a\n+band X 19c1 19c1 20160523 20302879 n/a\n+band X 19c2 19c2 20302879 20306293 n/a\n+band X 19c3 19c3 20306293 20321587 n/a\n+band X 19c4 19c4 20321587 20369792 n/a\n+band X 19c5 19c5 20369792 20391641 n/a\n+band X 19c6 19c6 20391641 20413490 n/a\n+band X 19d1 19d1 20413490 20481495 n/a\n+band X 19d2 19d2 20481495 20558345 n/a\n+band X 19d3 19d3 20558345 20604985 n/a\n+band X 19e1 19e1 20604985 20684138 n/a\n+band X 19e2 19e2 20684138 20763291 n/a\n+band X 19e3 19e3 20763291 20842444 n/a\n+band X 19e4 19e4 20842444 20921597 n/a\n+band X 19e5 19e5 20921597 20978999 n/a\n+band X 19e6 19e6 20978999 21014876 n/a\n+band X 19e7 19e7 21014876 21081024 n/a\n+band X 19e8 19e8 21081024 21086629 n/a\n+band X 19f1 19f1 21086629 21176545 n/a\n+band X 19f2 19f2 21176545 21266461 n/a\n+band X 19f3 19f3 21266461 21313101 n/a\n+band X 19f4 19f4 21313101 21338215 n/a\n+band X 19f5 19f5 21338215 21363329 n/a\n+band X 19f6 19f6 21363329 21377455 n/a\n+band X 20a1 20a1 21377455 21530155 n/a\n+band X 20a2 20a2 21530155 21535761 n/a\n+band X 20a3 20a3 21535761 21582401 n/a\n+band X 20a4 20a4 21582401 21629040 n/a\n+band X 20a5 20a5 21629040 21675680 n/a\n+band X 20c1 20c1 22371346 22545569 n/a\n+band X 20c2 20c2 22545569 22551175 n/a\n+band X 20c3 20c3 22551175 22597814 n/a\n+band X 20d1 20d1 22597814 22657235 n/a\n+band X 20d2 20d2 22657235 22716656 n/a\n+band X 20e1 20e1 22716656 22776077 n/a\n+band X 20e2 20e2 22776077 22835497 n/a\n+band X 20f1 20f1 22835497 22894918 n/a\n+band X 20f2 20f2 22894918 22954339 n/a\n+band X 20f3 20f3 22954339 23013760 n/a\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.drosophila.hires.dm3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.drosophila.hires.dm3.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,5056 @@\n+chr - dmX x 0 22422827 set1-6-qual-1\n+chr - dm2l 2l 0 22570260 set1-6-qual-2\n+chr - dm2r 2r 0 21146708 set1-6-qual-3\n+chr - dm3l 3l 0 23849507 set1-6-qual-4\n+chr - dm3r 3r 0 27905053 set1-6-qual-5\n+chr - dm4 4 0 1351857 set1-6-qual-6\n+band dm2l 21a5 21a5 0 22221 white\n+band dm2l 21b1 21b1 22221 98619 white\n+band dm2l 21b2 21b2 98619 134010 white\n+band dm2l 21b3 21b3 134010 161234 white\n+band dm2l 21b4 21b4 161234 213130 white\n+band dm2l 21b5 21b5 213130 256688 white\n+band dm2l 21b6 21b6 256688 267408 white\n+band dm2l 21b7 21b7 267408 294632 white\n+band dm2l 21b8 21b8 294632 324485 white\n+band dm2l 21c1 21c1 324485 390347 white\n+band dm2l 21c2 21c2 390347 456209 white\n+band dm2l 21c3 21c3 456209 456219 white\n+band dm2l 21c4 21c4 456219 456229 white\n+band dm2l 21c5 21c5 456229 456239 white\n+band dm2l 21c6 21c6 456239 456249 white\n+band dm2l 21c7 21c7 456249 458430 white\n+band dm2l 21c8 21c8 458430 464653 white\n+band dm2l 21d1 21d1 464653 482425 white\n+band dm2l 21d2 21d2 482425 500197 white\n+band dm2l 21d3 21d3 500197 510759 white\n+band dm2l 21d4 21d4 510759 518418 white\n+band dm2l 21e1 21e1 518418 533318 white\n+band dm2l 21e2 21e2 533318 987803 white\n+band dm2l 21e3 21e3 987803 1048634 white\n+band dm2l 21e4 21e4 1048634 1086654 white\n+band dm2l 21f1 21f1 1086654 1170535 white\n+band dm2l 21f2 21f2 1170535 1224563 white\n+band dm2l 21f3 21f3 1224563 1277401 white\n+band dm2l 21f4 21f4 1277401 1326937 white\n+band dm2l 22a1 22a1 1326937 1428804 white\n+band dm2l 22a2 22a2 1428804 1530671 white\n+band dm2l 22a3 22a3 1530671 1644731 white\n+band dm2l 22a4 22a4 1644731 1644741 white\n+band dm2l 22a5 22a5 1644741 1654988 white\n+band dm2l 22a6 22a6 1654988 1667727 white\n+band dm2l 22a7 22a7 1667727 1687818 white\n+band dm2l 22a8 22a8 1687818 1698637 white\n+band dm2l 22b1 22b1 1698637 1737370 white\n+band dm2l 22b2 22b2 1737370 1802684 white\n+band dm2l 22b3 22b3 1802684 1852361 white\n+band dm2l 22b4 22b4 1852361 1902039 white\n+band dm2l 22b5 22b5 1902039 1920281 white\n+band dm2l 22b6 22b6 1920281 1954160 white\n+band dm2l 22b7 22b7 1954160 1964421 white\n+band dm2l 22b8 22b8 1964421 2014098 white\n+band dm2l 22b9 22b9 2014098 2027808 white\n+band dm2l 22c1 22c1 2027808 2061629 white\n+band dm2l 22c2 22c2 2061629 2090832 white\n+band dm2l 22c3 22c3 2090832 2132199 white\n+band dm2l 22d1 22d1 2132199 2204105 white\n+band dm2l 22d2 22d2 2204105 2204115 white\n+band dm2l 22d3 22d3 2204115 2204125 white\n+band dm2l 22d4 22d4 2204125 2234802 white\n+band dm2l 22d5 22d5 2234802 2261169 white\n+band dm2l 22d6 22d6 2261169 2298835 white\n+band dm2l 22e1 22e1 2298835 2425019 white\n+band dm2l 22e2 22e2 2425019 2425029 white\n+band dm2l 22e3 22e3 2425029 2425039 white\n+band dm2l 22e4 22e4 2425039 2425049 white\n+band dm2l 22f1 22f1 2425049 2432797 white\n+band dm2l 22f2 22f2 2432797 2458422 white\n+band dm2l 22f3 22f3 2458422 2492448 white\n+band dm2l 22f4 22f4 2492448 2564558 white\n+band dm2l 23a1 23a1 2564558 2642867 white\n+band dm2l 23a2 23a2 2642867 2721176 white\n+band dm2l 23a3 23a3 2721176 2761795 white\n+band dm2l 23a4 23a4 2761795 2762015 white\n+band dm2l 23a5 23a5 2762015 2774487 white\n+band dm2l 23a6 23a6 2774487 2786959 white\n+band dm2l 23a7 23a7 2786959 2790737 white\n+band dm2l 23b1 23b1 2790737 2809025 white\n+band dm2l 23b2 23b2 2809025 2827313 white\n+band dm2l 23b3 23b3 2827313 2839785 white\n+band dm2l 23b4 23b4 2839785 2846501 white\n+band dm2l 23b5 23b5 2846501 2856095 white\n+band dm2l 23b6 23b6 2856095 2864302 white\n+band dm2l 23b7 23b7 2864302 2870047 white\n+band dm2l 23b8 23b8 2870047 2875792 white\n+band dm2l 23c1 23c1 2875792 2888923 white\n+band dm2l 23c2 23c2 2888923 2946983 white\n+band dm2l 23c3 23c3 2946983 2972384 white\n+band dm2l 23c4 23c4 2972384 3030443 white\n+band dm2l 23c5 23c5 3030443 3066730 white\n+band dm2l 23d1 23d1 3066730 3124790 white\n+band dm2l 23d2 23d2 3124790 3145048 white\n+band dm2l 23d3 23d3 3145048 3161507 white\n+band dm2l 23d4 23d4 3161507 3186062 white\n+band dm2l 23d5 23d5 3186062 3202164 white\n+band dm2l 23d6 2'..b'b4 19125173 19140255 white\n+band dmX 18b5 18b5 19140255 19143967 white\n+band dmX 18b6 18b6 19143967 19156222 white\n+band dmX 18b7 18b7 19156222 19168476 white\n+band dmX 18b8 18b8 19168476 19172188 white\n+band dmX 18b9 18b9 19172188 19178787 white\n+band dmX 18b10 18b10 19178787 19185386 white\n+band dmX 18b11 18b11 19185386 19189097 white\n+band dmX 18c1 18c1 19189097 19204180 white\n+band dmX 18c2 18c2 19204180 19236744 white\n+band dmX 18c3 18c3 19236744 19323371 white\n+band dmX 18c4 18c4 19323371 19326551 white\n+band dmX 18c5 18c5 19326551 19334565 white\n+band dmX 18c6 18c6 19334565 19361024 white\n+band dmX 18c7 18c7 19361024 19387483 white\n+band dmX 18c8 18c8 19387483 19449559 white\n+band dmX 18c9 18c9 19449559 19449569 white\n+band dmX 18d1 18d1 19449569 19464950 white\n+band dmX 18d2 18d2 19464950 19467194 white\n+band dmX 18d3 18d3 19467194 19510994 white\n+band dmX 18d4 18d4 19510994 19511004 white\n+band dmX 18d5 18d5 19511004 19511014 white\n+band dmX 18d6 18d6 19511014 19511217 white\n+band dmX 18d7 18d7 19511217 19519641 white\n+band dmX 18d8 18d8 19519641 19528066 white\n+band dmX 18d9 18d9 19528066 19528076 white\n+band dmX 18d10 18d10 19528076 19531583 white\n+band dmX 18d11 18d11 19531583 19538145 white\n+band dmX 18d12 18d12 19538145 19543193 white\n+band dmX 18d13 18d13 19543193 19570159 white\n+band dmX 18e1 18e1 19570159 19598262 white\n+band dmX 18e2 18e2 19598262 19600643 white\n+band dmX 18e3 18e3 19600643 19624078 white\n+band dmX 18e4 18e4 19624078 19626460 white\n+band dmX 18e5 18e5 19626460 19641702 white\n+band dmX 18f1 18f1 19641702 19675331 white\n+band dmX 18f2 18f2 19675331 19729986 white\n+band dmX 18f3 18f3 19729986 19745543 white\n+band dmX 18f4 18f4 19745543 19781104 white\n+band dmX 18f5 18f5 19781104 19781114 white\n+band dmX 19a1 19a1 19781114 19781124 white\n+band dmX 19a2 19a2 19781124 19816129 white\n+band dmX 19a3 19a3 19816129 19870888 white\n+band dmX 19a4 19a4 19870888 19925647 white\n+band dmX 19a5 19a5 19925647 19940941 white\n+band dmX 19a6 19a6 19940941 19962790 white\n+band dmX 19b1 19b1 19962790 20022738 white\n+band dmX 19b2 19b2 20022738 20026152 white\n+band dmX 19b3 19b3 20026152 20054556 white\n+band dmX 19c1 19c1 20054556 20173906 white\n+band dmX 19c2 19c2 20173906 20177320 white\n+band dmX 19c3 19c3 20177320 20192614 white\n+band dmX 19c4 19c4 20192614 20240819 white\n+band dmX 19c5 19c5 20240819 20262668 white\n+band dmX 19c6 19c6 20262668 20284517 white\n+band dmX 19d1 19d1 20284517 20352522 white\n+band dmX 19d2 19d2 20352522 20429372 white\n+band dmX 19d3 19d3 20429372 20476012 white\n+band dmX 19e1 19e1 20476012 20555165 white\n+band dmX 19e2 19e2 20555165 20634318 white\n+band dmX 19e3 19e3 20634318 20713471 white\n+band dmX 19e4 19e4 20713471 20792624 white\n+band dmX 19e5 19e5 20792624 20850026 white\n+band dmX 19e6 19e6 20850026 20885903 white\n+band dmX 19e7 19e7 20885903 20952051 white\n+band dmX 19e8 19e8 20952051 20957656 white\n+band dmX 19f1 19f1 20957656 21047572 white\n+band dmX 19f2 19f2 21047572 21137488 white\n+band dmX 19f3 19f3 21137488 21184128 white\n+band dmX 19f4 19f4 21184128 21209242 white\n+band dmX 19f5 19f5 21209242 21234356 white\n+band dmX 19f6 19f6 21234356 21248482 white\n+band dmX 20a1 20a1 21248482 21401182 white\n+band dmX 20a2 20a2 21401182 21406788 white\n+band dmX 20a3 20a3 21406788 21453428 white\n+band dmX 20a4 20a4 21453428 21500067 white\n+band dmX 20a5 20a5 21500067 21546707 white\n+band dmX 20b1 20b1 21546707 21720933 white\n+band dmX 20b2 20b2 21720933 21726539 white\n+band dmX 20b3 20b3 21726539 21773179 white\n+band dmX 20c1 20c1 21773179 21947405 white\n+band dmX 20c2 20c2 21947405 21953011 white\n+band dmX 20c3 20c3 21953011 21999650 white\n+band dmX 20d1 20d1 21999650 22059071 white\n+band dmX 20d2 20d2 22059071 22118492 white\n+band dmX 20e1 20e1 22118492 22177913 white\n+band dmX 20e2 20e2 22177913 22237333 white\n+band dmX 20f1 20f1 22237333 22296754 white\n+band dmX 20f2 20f2 22296754 22356175 white\n+band dmX 20f3 20f3 22356175 22415596 white\n+band dmX 20f4 20f4 22415596 22422827 white\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.human.hg16.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.human.hg16.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,886 @@\n+chr - hsX X 0 153692391 chrx\n+chr - hsY Y 0 50286555 chry\n+chr - hs1 1 0 246127941 chr1\n+chr - hs2 2 0 243615958 chr2\n+chr - hs3 3 0 199344050 chr3\n+chr - hs4 4 0 191731959 chr4\n+chr - hs5 5 0 181034922 chr5\n+chr - hs6 6 0 170914576 chr6\n+chr - hs7 7 0 158545518 chr7\n+chr - hs8 8 0 146308819 chr8\n+chr - hs9 9 0 136372045 chr9\n+chr - hs10 10 0 135037215 chr10\n+chr - hs11 11 0 134482954 chr11\n+chr - hs12 12 0 132078379 chr12\n+chr - hs13 13 0 113042980 chr13\n+chr - hs14 14 0 105311216 chr14\n+chr - hs15 15 0 100256656 chr15\n+chr - hs16 16 0 90041932 chr16\n+chr - hs17 17 0 81860266 chr17\n+chr - hs18 18 0 76115139 chr18\n+chr - hs19 19 0 63811651 chr19\n+chr - hs20 20 0 63741868 chr20\n+chr - hs21 21 0 46976097 chr21\n+chr - hs22 22 0 49396972 chr22\n+band hs1 p36.33 p36.33 0 2200000 gneg\n+band hs1 p36.32 p36.32 2200000 5100000 gpos25\n+band hs1 p36.31 p36.31 5100000 6900000 gneg\n+band hs1 p36.23 p36.23 6900000 8800000 gpos25\n+band hs1 p36.22 p36.22 8800000 12100000 gneg\n+band hs1 p36.21 p36.21 12100000 15200000 gpos50\n+band hs1 p36.13 p36.13 15200000 19900000 gneg\n+band hs1 p36.12 p36.12 19900000 23400000 gpos25\n+band hs1 p36.11 p36.11 23400000 27600000 gneg\n+band hs1 p35.3 p35.3 27600000 30000000 gpos25\n+band hs1 p35.2 p35.2 30000000 32300000 gneg\n+band hs1 p35.1 p35.1 32300000 34300000 gpos25\n+band hs1 p34.3 p34.3 34300000 39600000 gneg\n+band hs1 p34.2 p34.2 39600000 43600000 gpos25\n+band hs1 p34.1 p34.1 43600000 46100000 gneg\n+band hs1 p33 p33 46100000 50100000 gpos75\n+band hs1 p32.3 p32.3 50100000 55400000 gneg\n+band hs1 p32.2 p32.2 55400000 58300000 gpos50\n+band hs1 p32.1 p32.1 58300000 60600000 gneg\n+band hs1 p31.3 p31.3 60600000 65100000 gpos50\n+band hs1 p31.2 p31.2 65100000 69100000 gneg\n+band hs1 p31.1 p31.1 69100000 84300000 gpos100\n+band hs1 p22.3 p22.3 84300000 87800000 gneg\n+band hs1 p22.2 p22.2 87800000 91500000 gpos75\n+band hs1 p22.1 p22.1 91500000 94200000 gneg\n+band hs1 p21.3 p21.3 94200000 99100000 gpos75\n+band hs1 p21.2 p21.2 99100000 101600000 gneg\n+band hs1 p21.1 p21.1 101600000 106600000 gpos100\n+band hs1 p13.3 p13.3 106600000 111100000 gneg\n+band hs1 p13.2 p13.2 111100000 114500000 gpos50\n+band hs1 p13.1 p13.1 114500000 117100000 gneg\n+band hs1 p12 p12 117100000 119700000 gpos50\n+band hs1 p11.2 p11.2 119700000 120000000 gneg\n+band hs1 p11.1 p11.1 120000000 123200000 acen\n+band hs1 q11 q11 123200000 126900000 acen\n+band hs1 q12 q12 126900000 140800000 gvar\n+band hs1 q21.1 q21.1 140800000 145900000 gneg\n+band hs1 q21.2 q21.2 145900000 148000000 gpos50\n+band hs1 q21.3 q21.3 148000000 151500000 gneg\n+band hs1 q22 q22 151500000 153700000 gpos50\n+band hs1 q23.1 q23.1 153700000 156300000 gneg\n+band hs1 q23.2 q23.2 156300000 157700000 gpos50\n+band hs1 q23.3 q23.3 157700000 162700000 gneg\n+band hs1 q24.1 q24.1 162700000 164400000 gpos50\n+band hs1 q24.2 q24.2 164400000 168100000 gneg\n+band hs1 q24.3 q24.3 168100000 170200000 gpos75\n+band hs1 q25.1 q25.1 170200000 173300000 gneg\n+band hs1 q25.2 q25.2 173300000 177500000 gpos50\n+band hs1 q25.3 q25.3 177500000 183000000 gneg\n+band hs1 q31.1 q31.1 183000000 188000000 gpos100\n+band hs1 q31.2 q31.2 188000000 191000000 gneg\n+band hs1 q31.3 q31.3 191000000 195900000 gpos100\n+band hs1 q32.1 q32.1 195900000 204300000 gneg\n+band hs1 q32.2 q32.2 204300000 208500000 gpos25\n+band hs1 q32.3 q32.3 208500000 211600000 gneg\n+band hs1 q41 q41 211600000 220500000 gpos100\n+band hs1 q42.11 q42.11 220500000 221400000 gneg\n+band hs1 q42.12 q42.12 221400000 224000000 gpos25\n+band hs1 q42.13 q42.13 224000000 227700000 gneg\n+band hs1 q42.2 q42.2 227700000 231800000 gpos50\n+band hs1 q42.3 q42.3 231800000 233600000 gneg\n+band hs1 q43 q43 233600000 240000000 gpos75\n+band hs1 q44 q44 240000000 246127941 gneg\n+band hs10 p15.3 p15.3 0 3000000 gneg\n+band hs10 p15.2 p15.2 3000000 3800000 gpos25\n+band hs10 p15.1 p15.1 3800000 6600000 gneg\n+band hs10 p14 p14 6600000 12200000 gpos75\n+band hs10 p13 p13 12200000 17300000 gneg\n+band hs10 p12.33 p12.33 17300000 18600000 gpos75\n+band hs10 p12.32 p'..b'\n+band hs9 p21.2 p21.2 25500000 28100000 gneg\n+band hs9 p21.1 p21.1 28100000 33200000 gpos100\n+band hs9 p13.3 p13.3 33200000 36300000 gneg\n+band hs9 p13.2 p13.2 36300000 37900000 gpos25\n+band hs9 p13.1 p13.1 37900000 39700000 gneg\n+band hs9 p12 p12 39700000 41400000 gpos50\n+band hs9 p11.2 p11.2 41400000 44300000 gneg\n+band hs9 p11.1 p11.1 44300000 49000000 acen\n+band hs9 q11 q11 49000000 57600000 acen\n+band hs9 q12 q12 57600000 62900000 gvar\n+band hs9 q13 q13 62900000 65800000 gneg\n+band hs9 q21.11 q21.11 65800000 69400000 gpos25\n+band hs9 q21.12 q21.12 69400000 71200000 gneg\n+band hs9 q21.13 q21.13 71200000 74700000 gpos50\n+band hs9 q21.2 q21.2 74700000 76500000 gneg\n+band hs9 q21.31 q21.31 76500000 79600000 gpos50\n+band hs9 q21.32 q21.32 79600000 82400000 gneg\n+band hs9 q21.33 q21.33 82400000 85800000 gpos50\n+band hs9 q22.1 q22.1 85800000 87300000 gneg\n+band hs9 q22.2 q22.2 87300000 89300000 gpos25\n+band hs9 q22.31 q22.31 89300000 92100000 gneg\n+band hs9 q22.32 q22.32 92100000 94900000 gpos25\n+band hs9 q22.33 q22.33 94900000 98300000 gneg\n+band hs9 q31.1 q31.1 98300000 103800000 gpos100\n+band hs9 q31.2 q31.2 103800000 106800000 gneg\n+band hs9 q31.3 q31.3 106800000 110300000 gpos25\n+band hs9 q32 q32 110300000 113100000 gneg\n+band hs9 q33.1 q33.1 113100000 117900000 gpos75\n+band hs9 q33.2 q33.2 117900000 121200000 gneg\n+band hs9 q33.3 q33.3 121200000 125600000 gpos25\n+band hs9 q34.11 q34.11 125600000 128800000 gneg\n+band hs9 q34.12 q34.12 128800000 129100000 gpos25\n+band hs9 q34.13 q34.13 129100000 131200000 gneg\n+band hs9 q34.2 q34.2 131200000 132900000 gpos25\n+band hs9 q34.3 q34.3 132900000 136372045 gneg\n+band hsX p22.33 p22.33 0 4000000 gneg\n+band hsX p22.32 p22.32 4000000 5400000 gpos50\n+band hsX p22.31 p22.31 5400000 8900000 gneg\n+band hsX p22.22 p22.22 8900000 16800000 gpos50\n+band hsX p22.13 p22.13 16800000 18600000 gneg\n+band hsX p22.12 p22.12 18600000 21300000 gpos50\n+band hsX p22.11 p22.11 21300000 24400000 gneg\n+band hsX p21.3 p21.3 24400000 28800000 gpos100\n+band hsX p21.2 p21.2 28800000 30900000 gneg\n+band hsX p21.1 p21.1 30900000 36700000 gpos100\n+band hsX p11.4 p11.4 36700000 41400000 gneg\n+band hsX p11.3 p11.3 41400000 46500000 gpos75\n+band hsX p11.23 p11.23 46500000 48800000 gneg\n+band hsX p11.22 p11.22 48800000 53600000 gpos25\n+band hsX p11.21 p11.21 53600000 55600000 gneg\n+band hsX p11.1 p11.1 55600000 58500000 acen\n+band hsX q11.1 q11.1 58500000 60600000 acen\n+band hsX q11.2 q11.2 60600000 63100000 gneg\n+band hsX q12 q12 63100000 66600000 gpos50\n+band hsX q13.1 q13.1 66600000 71100000 gneg\n+band hsX q13.2 q13.2 71100000 72800000 gpos50\n+band hsX q13.3 q13.3 72800000 74900000 gneg\n+band hsX q21.1 q21.1 74900000 83400000 gpos100\n+band hsX q21.2 q21.2 83400000 85100000 gneg\n+band hsX q21.31 q21.31 85100000 90800000 gpos100\n+band hsX q21.32 q21.32 90800000 92500000 gneg\n+band hsX q21.33 q21.33 92500000 97100000 gpos75\n+band hsX q22.1 q22.1 97100000 101400000 gneg\n+band hsX q22.2 q22.2 101400000 102500000 gpos50\n+band hsX q22.3 q22.3 102500000 107400000 gneg\n+band hsX q23 q23 107400000 115300000 gpos75\n+band hsX q24 q24 115300000 119600000 gneg\n+band hsX q25 q25 119600000 127400000 gpos100\n+band hsX q26.1 q26.1 127400000 129100000 gneg\n+band hsX q26.2 q26.2 129100000 132400000 gpos25\n+band hsX q26.3 q26.3 132400000 136700000 gneg\n+band hsX q27.1 q27.1 136700000 139000000 gpos75\n+band hsX q27.2 q27.2 139000000 140700000 gneg\n+band hsX q27.3 q27.3 140700000 145800000 gpos100\n+band hsX q28 q28 145800000 153692391 gneg\n+band hsY p11.32 p11.32 0 1300000 gneg\n+band hsY p11.31 p11.31 1300000 2600000 gpos50\n+band hsY p11.2 p11.2 2600000 9700000 gneg\n+band hsY p11.1 p11.1 9700000 10700000 acen\n+band hsY q11.1 q11.1 10700000 12800000 acen\n+band hsY q11.21 q11.21 12800000 14800000 gneg\n+band hsY q11.221 q11.221 14800000 19300000 gpos50\n+band hsY q11.222 q11.222 19300000 21800000 gneg\n+band hsY q11.223 q11.223 21800000 25800000 gpos50\n+band hsY q11.23 q11.23 25800000 27700000 gneg\n+band hsY q12 q12 27700000 50286555 gvar\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.human.hg17.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.human.hg17.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,886 @@\n+chr - hsx x 0 154824264 chrx\n+chr - hsY y 0 57701691 chry\n+chr - hs1 1 0 245522847 chr1\n+chr - hs2 2 0 243018229 chr2\n+chr - hs3 3 0 199505740 chr3\n+chr - hs4 4 0 191411218 chr4\n+chr - hs5 5 0 180857866 chr5\n+chr - hs6 6 0 170975699 chr6\n+chr - hs7 7 0 158628139 chr7\n+chr - hs8 8 0 146274826 chr8\n+chr - hs9 9 0 138429268 chr9\n+chr - hs10 10 0 135413628 chr10\n+chr - hs11 11 0 134452384 chr11\n+chr - hs12 12 0 132449811 chr12\n+chr - hs13 13 0 114142980 chr13\n+chr - hs14 14 0 106368585 chr14\n+chr - hs15 15 0 100338915 chr15\n+chr - hs16 16 0 88827254 chr16\n+chr - hs17 17 0 78774742 chr17\n+chr - hs18 18 0 76117153 chr18\n+chr - hs19 19 0 63811651 chr19\n+chr - hs20 20 0 62435964 chr20\n+chr - hs21 21 0 46944323 chr21\n+chr - hs22 22 0 49554710 chr22\n+band hs1 p36.33 p36.33 0 2300000 gneg\n+band hs1 p36.32 p36.32 2300000 5300000 gpos25\n+band hs1 p36.31 p36.31 5300000 7100000 gneg\n+band hs1 p36.23 p36.23 7100000 9000000 gpos25\n+band hs1 p36.22 p36.22 9000000 12300000 gneg\n+band hs1 p36.21 p36.21 12300000 15600000 gpos50\n+band hs1 p36.13 p36.13 15600000 20200000 gneg\n+band hs1 p36.12 p36.12 20200000 23700000 gpos25\n+band hs1 p36.11 p36.11 23700000 27700000 gneg\n+band hs1 p35.3 p35.3 27700000 30000000 gpos25\n+band hs1 p35.2 p35.2 30000000 32100000 gneg\n+band hs1 p35.1 p35.1 32100000 34300000 gpos25\n+band hs1 p34.3 p34.3 34300000 39800000 gneg\n+band hs1 p34.2 p34.2 39800000 43800000 gpos25\n+band hs1 p34.1 p34.1 43800000 46500000 gneg\n+band hs1 p33 p33 46500000 50400000 gpos75\n+band hs1 p32.3 p32.3 50400000 55800000 gneg\n+band hs1 p32.2 p32.2 55800000 58700000 gpos50\n+band hs1 p32.1 p32.1 58700000 60100000 gneg\n+band hs1 p31.3 p31.3 60100000 65500000 gpos50\n+band hs1 p31.2 p31.2 65500000 69500000 gneg\n+band hs1 p31.1 p31.1 69500000 84600000 gpos100\n+band hs1 p22.3 p22.3 84600000 88100000 gneg\n+band hs1 p22.2 p22.2 88100000 91700000 gpos75\n+band hs1 p22.1 p22.1 91700000 94500000 gneg\n+band hs1 p21.3 p21.3 94500000 99500000 gpos75\n+band hs1 p21.2 p21.2 99500000 102000000 gneg\n+band hs1 p21.1 p21.1 102000000 106900000 gpos100\n+band hs1 p13.3 p13.3 106900000 111500000 gneg\n+band hs1 p13.2 p13.2 111500000 114900000 gpos50\n+band hs1 p13.1 p13.1 114900000 117500000 gneg\n+band hs1 p12 p12 117500000 120300000 gpos50\n+band hs1 p11.2 p11.2 120300000 121000000 gneg\n+band hs1 p11.1 p11.1 121000000 124200000 acen\n+band hs1 q11 q11 124200000 127900000 acen\n+band hs1 q12 q12 127900000 141600000 gvar\n+band hs1 q21.1 q21.1 141600000 146500000 gneg\n+band hs1 q21.2 q21.2 146500000 148100000 gpos50\n+band hs1 q21.3 q21.3 148100000 151400000 gneg\n+band hs1 q22 q22 151400000 153400000 gpos50\n+band hs1 q23.1 q23.1 153400000 155900000 gneg\n+band hs1 q23.2 q23.2 155900000 157300000 gpos50\n+band hs1 q23.3 q23.3 157300000 162300000 gneg\n+band hs1 q24.1 q24.1 162300000 163900000 gpos50\n+band hs1 q24.2 q24.2 163900000 167600000 gneg\n+band hs1 q24.3 q24.3 167600000 169700000 gpos75\n+band hs1 q25.1 q25.1 169700000 172800000 gneg\n+band hs1 q25.2 q25.2 172800000 177000000 gpos50\n+band hs1 q25.3 q25.3 177000000 182500000 gneg\n+band hs1 q31.1 q31.1 182500000 187500000 gpos100\n+band hs1 q31.2 q31.2 187500000 190500000 gneg\n+band hs1 q31.3 q31.3 190500000 196000000 gpos100\n+band hs1 q32.1 q32.1 196000000 203600000 gneg\n+band hs1 q32.2 q32.2 203600000 207800000 gpos25\n+band hs1 q32.3 q32.3 207800000 210500000 gneg\n+band hs1 q41 q41 210500000 219800000 gpos100\n+band hs1 q42.11 q42.11 219800000 220600000 gneg\n+band hs1 q42.12 q42.12 220600000 223300000 gpos25\n+band hs1 q42.13 q42.13 223300000 227000000 gneg\n+band hs1 q42.2 q42.2 227000000 231000000 gpos50\n+band hs1 q42.3 q42.3 231000000 232900000 gneg\n+band hs1 q43 q43 232900000 239500000 gpos75\n+band hs1 q44 q44 239500000 245522847 gneg\n+band hs10 p15.3 p15.3 0 3000000 gneg\n+band hs10 p15.2 p15.2 3000000 3800000 gpos25\n+band hs10 p15.1 p15.1 3800000 6700000 gneg\n+band hs10 p14 p14 6700000 12300000 gpos75\n+band hs10 p13 p13 12300000 17300000 gneg\n+band hs10 p12.33 p12.33 17300000 18600000 gpos75\n+band hs10 p12.32 p'..b'\n+band hs9 p21.2 p21.2 25500000 28100000 gneg\n+band hs9 p21.1 p21.1 28100000 33200000 gpos100\n+band hs9 p13.3 p13.3 33200000 36200000 gneg\n+band hs9 p13.2 p13.2 36200000 38600000 gpos25\n+band hs9 p13.1 p13.1 38600000 41400000 gneg\n+band hs9 p12 p12 41400000 44200000 gpos50\n+band hs9 p11.2 p11.2 44200000 45900000 gneg\n+band hs9 p11.1 p11.1 45900000 50600000 acen\n+band hs9 q11 q11 50600000 59200000 acen\n+band hs9 q12 q12 59200000 67500000 gvar\n+band hs9 q13 q13 67500000 68600000 gneg\n+band hs9 q21.11 q21.11 68600000 70800000 gpos25\n+band hs9 q21.12 q21.12 70800000 71200000 gneg\n+band hs9 q21.13 q21.13 71200000 76400000 gpos50\n+band hs9 q21.2 q21.2 76400000 78300000 gneg\n+band hs9 q21.31 q21.31 78300000 81300000 gpos50\n+band hs9 q21.32 q21.32 81300000 84100000 gneg\n+band hs9 q21.33 q21.33 84100000 87600000 gpos50\n+band hs9 q22.1 q22.1 87600000 89000000 gneg\n+band hs9 q22.2 q22.2 89000000 91000000 gpos25\n+band hs9 q22.31 q22.31 91000000 93700000 gneg\n+band hs9 q22.32 q22.32 93700000 96300000 gpos25\n+band hs9 q22.33 q22.33 96300000 99600000 gneg\n+band hs9 q31.1 q31.1 99600000 105300000 gpos100\n+band hs9 q31.2 q31.2 105300000 108400000 gneg\n+band hs9 q31.3 q31.3 108400000 112000000 gpos25\n+band hs9 q32 q32 112000000 114800000 gneg\n+band hs9 q33.1 q33.1 114800000 119600000 gpos75\n+band hs9 q33.2 q33.2 119600000 122900000 gneg\n+band hs9 q33.3 q33.3 122900000 127300000 gpos25\n+band hs9 q34.11 q34.11 127300000 130500000 gneg\n+band hs9 q34.12 q34.12 130500000 130900000 gpos25\n+band hs9 q34.13 q34.13 130900000 133000000 gneg\n+band hs9 q34.2 q34.2 133000000 134700000 gpos25\n+band hs9 q34.3 q34.3 134700000 138429268 gneg\n+band hsx p22.33 p22.33 0 4200000 gneg\n+band hsx p22.32 p22.32 4200000 5800000 gpos50\n+band hsx p22.31 p22.31 5800000 9300000 gneg\n+band hsx p22.2 p22.2 9300000 17200000 gpos50\n+band hsx p22.13 p22.13 17200000 19000000 gneg\n+band hsx p22.12 p22.12 19000000 21600000 gpos50\n+band hsx p22.11 p22.11 21600000 24700000 gneg\n+band hsx p21.3 p21.3 24700000 29200000 gpos100\n+band hsx p21.2 p21.2 29200000 31300000 gneg\n+band hsx p21.1 p21.1 31300000 37400000 gpos100\n+band hsx p11.4 p11.4 37400000 42100000 gneg\n+band hsx p11.3 p11.3 42100000 47200000 gpos75\n+band hsx p11.23 p11.23 47200000 49500000 gneg\n+band hsx p11.22 p11.22 49500000 54500000 gpos25\n+band hsx p11.21 p11.21 54500000 56500000 gneg\n+band hsx p11.1 p11.1 56500000 59400000 acen\n+band hsx q11.1 q11.1 59400000 61500000 acen\n+band hsx q11.2 q11.2 61500000 64000000 gneg\n+band hsx q12 q12 64000000 67500000 gpos50\n+band hsx q13.1 q13.1 67500000 72000000 gneg\n+band hsx q13.2 q13.2 72000000 73700000 gpos50\n+band hsx q13.3 q13.3 73700000 75800000 gneg\n+band hsx q21.1 q21.1 75800000 84400000 gpos100\n+band hsx q21.2 q21.2 84400000 86100000 gneg\n+band hsx q21.31 q21.31 86100000 91800000 gpos100\n+band hsx q21.32 q21.32 91800000 93500000 gneg\n+band hsx q21.33 q21.33 93500000 98200000 gpos75\n+band hsx q22.1 q22.1 98200000 102400000 gneg\n+band hsx q22.2 q22.2 102400000 103500000 gpos50\n+band hsx q22.3 q22.3 103500000 108500000 gneg\n+band hsx q23 q23 108500000 116300000 gpos75\n+band hsx q24 q24 116300000 120600000 gneg\n+band hsx q25 q25 120600000 129700000 gpos100\n+band hsx q26.1 q26.1 129700000 130200000 gneg\n+band hsx q26.2 q26.2 130200000 133400000 gpos25\n+band hsx q26.3 q26.3 133400000 137700000 gneg\n+band hsx q27.1 q27.1 137700000 140000000 gpos75\n+band hsx q27.2 q27.2 140000000 141800000 gneg\n+band hsx q27.3 q27.3 141800000 146800000 gpos100\n+band hsx q28 q28 146800000 154824264 gneg\n+band hsY p11.32 p11.32 0 1700000 gneg\n+band hsY p11.31 p11.31 1700000 3300000 gpos50\n+band hsY p11.2 p11.2 3300000 11200000 gneg\n+band hsY p11.1 p11.1 11200000 11500000 acen\n+band hsY q11.1 q11.1 11500000 12400000 acen\n+band hsY q11.21 q11.21 12400000 14200000 gneg\n+band hsY q11.221 q11.221 14200000 18800000 gpos50\n+band hsY q11.222 q11.222 18800000 21100000 gneg\n+band hsY q11.223 q11.223 21100000 25200000 gpos50\n+band hsY q11.23 q11.23 25200000 27100000 gneg\n+band hsY q12 q12 27100000 57701691 gvar\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.human.hg18.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.human.hg18.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,886 @@\n+chr - hs1 1 0 247249719 chr1\n+chr - hs2 2 0 242951149 chr2\n+chr - hs3 3 0 199501827 chr3\n+chr - hs4 4 0 191273063 chr4\n+chr - hs5 5 0 180857866 chr5\n+chr - hs6 6 0 170899992 chr6\n+chr - hs7 7 0 158821424 chr7\n+chr - hs8 8 0 146274826 chr8\n+chr - hs9 9 0 140273252 chr9\n+chr - hs10 10 0 135374737 chr10\n+chr - hs11 11 0 134452384 chr11\n+chr - hs12 12 0 132349534 chr12\n+chr - hs13 13 0 114142980 chr13\n+chr - hs14 14 0 106368585 chr14\n+chr - hs15 15 0 100338915 chr15\n+chr - hs16 16 0 88827254 chr16\n+chr - hs17 17 0 78774742 chr17\n+chr - hs18 18 0 76117153 chr18\n+chr - hs19 19 0 63811651 chr19\n+chr - hs20 20 0 62435964 chr20\n+chr - hs21 21 0 46944323 chr21\n+chr - hs22 22 0 49691432 chr22\n+chr - hsX x 0 154913754 chrx\n+chr - hsY y 0 57772954 chry\n+band hs1 p36.33 p36.33 0 2300000 gneg\n+band hs1 p36.32 p36.32 2300000 5300000 gpos25\n+band hs1 p36.31 p36.31 5300000 7100000 gneg\n+band hs1 p36.23 p36.23 7100000 9200000 gpos25\n+band hs1 p36.22 p36.22 9200000 12600000 gneg\n+band hs1 p36.21 p36.21 12600000 16100000 gpos50\n+band hs1 p36.13 p36.13 16100000 20300000 gneg\n+band hs1 p36.12 p36.12 20300000 23800000 gpos25\n+band hs1 p36.11 p36.11 23800000 27800000 gneg\n+band hs1 p35.3 p35.3 27800000 30000000 gpos25\n+band hs1 p35.2 p35.2 30000000 32200000 gneg\n+band hs1 p35.1 p35.1 32200000 34400000 gpos25\n+band hs1 p34.3 p34.3 34400000 39600000 gneg\n+band hs1 p34.2 p34.2 39600000 43900000 gpos25\n+band hs1 p34.1 p34.1 43900000 46500000 gneg\n+band hs1 p33 p33 46500000 51300000 gpos75\n+band hs1 p32.3 p32.3 51300000 56200000 gneg\n+band hs1 p32.2 p32.2 56200000 58700000 gpos50\n+band hs1 p32.1 p32.1 58700000 60900000 gneg\n+band hs1 p31.3 p31.3 60900000 68700000 gpos50\n+band hs1 p31.2 p31.2 68700000 69500000 gneg\n+band hs1 p31.1 p31.1 69500000 84700000 gpos100\n+band hs1 p22.3 p22.3 84700000 88100000 gneg\n+band hs1 p22.2 p22.2 88100000 92000000 gpos75\n+band hs1 p22.1 p22.1 92000000 94500000 gneg\n+band hs1 p21.3 p21.3 94500000 99400000 gpos75\n+band hs1 p21.2 p21.2 99400000 102000000 gneg\n+band hs1 p21.1 p21.1 102000000 107000000 gpos100\n+band hs1 p13.3 p13.3 107000000 111600000 gneg\n+band hs1 p13.2 p13.2 111600000 115900000 gpos50\n+band hs1 p13.1 p13.1 115900000 117600000 gneg\n+band hs1 p12 p12 117600000 120700000 gpos50\n+band hs1 p11.2 p11.2 120700000 121100000 gneg\n+band hs1 p11.1 p11.1 121100000 124300000 acen\n+band hs1 q11 q11 124300000 128000000 acen\n+band hs1 q12 q12 128000000 142400000 gvar\n+band hs1 q21.1 q21.1 142400000 148000000 gneg\n+band hs1 q21.2 q21.2 148000000 149600000 gpos50\n+band hs1 q21.3 q21.3 149600000 153300000 gneg\n+band hs1 q22 q22 153300000 154800000 gpos50\n+band hs1 q23.1 q23.1 154800000 157300000 gneg\n+band hs1 q23.2 q23.2 157300000 158800000 gpos50\n+band hs1 q23.3 q23.3 158800000 163800000 gneg\n+band hs1 q24.1 q24.1 163800000 165500000 gpos50\n+band hs1 q24.2 q24.2 165500000 169100000 gneg\n+band hs1 q24.3 q24.3 169100000 171200000 gpos75\n+band hs1 q25.1 q25.1 171200000 174300000 gneg\n+band hs1 q25.2 q25.2 174300000 178600000 gpos50\n+band hs1 q25.3 q25.3 178600000 184000000 gneg\n+band hs1 q31.1 q31.1 184000000 189000000 gpos100\n+band hs1 q31.2 q31.2 189000000 192100000 gneg\n+band hs1 q31.3 q31.3 192100000 197500000 gpos100\n+band hs1 q32.1 q32.1 197500000 205300000 gneg\n+band hs1 q32.2 q32.2 205300000 209500000 gpos25\n+band hs1 q32.3 q32.3 209500000 212100000 gneg\n+band hs1 q41 q41 212100000 222100000 gpos100\n+band hs1 q42.11 q42.11 222100000 222700000 gneg\n+band hs1 q42.12 q42.12 222700000 225100000 gpos25\n+band hs1 q42.13 q42.13 225100000 228800000 gneg\n+band hs1 q42.2 q42.2 228800000 232700000 gpos50\n+band hs1 q42.3 q42.3 232700000 234600000 gneg\n+band hs1 q43 q43 234600000 241700000 gpos75\n+band hs1 q44 q44 241700000 247249719 gneg\n+band hs10 p15.3 p15.3 0 3000000 gneg\n+band hs10 p15.2 p15.2 3000000 3800000 gpos25\n+band hs10 p15.1 p15.1 3800000 6700000 gneg\n+band hs10 p14 p14 6700000 12300000 gpos75\n+band hs10 p13 p13 12300000 17300000 gneg\n+band hs10 p12.33 p12.33 17300000 19900000 gpos75\n+band hs10 p12.32 p'..b'band hs9 p21.2 p21.2 25500000 28100000 gneg\n+band hs9 p21.1 p21.1 28100000 32800000 gpos100\n+band hs9 p13.3 p13.3 32800000 36300000 gneg\n+band hs9 p13.2 p13.2 36300000 38000000 gpos25\n+band hs9 p13.1 p13.1 38000000 40200000 gneg\n+band hs9 p12 p12 40200000 42400000 gpos50\n+band hs9 p11.2 p11.2 42400000 46700000 gneg\n+band hs9 p11.1 p11.1 46700000 51800000 acen\n+band hs9 q11 q11 51800000 60300000 acen\n+band hs9 q12 q12 60300000 70000000 gvar\n+band hs9 q13 q13 70000000 70500000 gneg\n+band hs9 q21.11 q21.11 70500000 72700000 gpos25\n+band hs9 q21.12 q21.12 72700000 73100000 gneg\n+band hs9 q21.13 q21.13 73100000 79300000 gpos50\n+band hs9 q21.2 q21.2 79300000 80300000 gneg\n+band hs9 q21.31 q21.31 80300000 83400000 gpos50\n+band hs9 q21.32 q21.32 83400000 86100000 gneg\n+band hs9 q21.33 q21.33 86100000 89600000 gpos50\n+band hs9 q22.1 q22.1 89600000 91000000 gneg\n+band hs9 q22.2 q22.2 91000000 93000000 gpos25\n+band hs9 q22.31 q22.31 93000000 95600000 gneg\n+band hs9 q22.32 q22.32 95600000 98200000 gpos25\n+band hs9 q22.33 q22.33 98200000 101600000 gneg\n+band hs9 q31.1 q31.1 101600000 107200000 gpos100\n+band hs9 q31.2 q31.2 107200000 110300000 gneg\n+band hs9 q31.3 q31.3 110300000 113900000 gpos25\n+band hs9 q32 q32 113900000 116700000 gneg\n+band hs9 q33.1 q33.1 116700000 122000000 gpos75\n+band hs9 q33.2 q33.2 122000000 125800000 gneg\n+band hs9 q33.3 q33.3 125800000 129300000 gpos25\n+band hs9 q34.11 q34.11 129300000 132500000 gneg\n+band hs9 q34.12 q34.12 132500000 132800000 gpos25\n+band hs9 q34.13 q34.13 132800000 134900000 gneg\n+band hs9 q34.2 q34.2 134900000 136600000 gpos25\n+band hs9 q34.3 q34.3 136600000 140273252 gneg\n+band hsX p22.33 p22.33 0 4300000 gneg\n+band hsX p22.32 p22.32 4300000 6000000 gpos50\n+band hsX p22.31 p22.31 6000000 9500000 gneg\n+band hsX p22.2 p22.2 9500000 17100000 gpos50\n+band hsX p22.13 p22.13 17100000 19200000 gneg\n+band hsX p22.12 p22.12 19200000 21800000 gpos50\n+band hsX p22.11 p22.11 21800000 24900000 gneg\n+band hsX p21.3 p21.3 24900000 29400000 gpos100\n+band hsX p21.2 p21.2 29400000 31500000 gneg\n+band hsX p21.1 p21.1 31500000 37500000 gpos100\n+band hsX p11.4 p11.4 37500000 42300000 gneg\n+band hsX p11.3 p11.3 42300000 47300000 gpos75\n+band hsX p11.23 p11.23 47300000 49700000 gneg\n+band hsX p11.22 p11.22 49700000 54700000 gpos25\n+band hsX p11.21 p11.21 54700000 56600000 gneg\n+band hsX p11.1 p11.1 56600000 59500000 acen\n+band hsX q11.1 q11.1 59500000 65000000 acen\n+band hsX q11.2 q11.2 65000000 65100000 gneg\n+band hsX q12 q12 65100000 67700000 gpos50\n+band hsX q13.1 q13.1 67700000 72200000 gneg\n+band hsX q13.2 q13.2 72200000 73800000 gpos50\n+band hsX q13.3 q13.3 73800000 76000000 gneg\n+band hsX q21.1 q21.1 76000000 84500000 gpos100\n+band hsX q21.2 q21.2 84500000 86200000 gneg\n+band hsX q21.31 q21.31 86200000 91900000 gpos100\n+band hsX q21.32 q21.32 91900000 93500000 gneg\n+band hsX q21.33 q21.33 93500000 98200000 gpos75\n+band hsX q22.1 q22.1 98200000 102500000 gneg\n+band hsX q22.2 q22.2 102500000 103600000 gpos50\n+band hsX q22.3 q22.3 103600000 110500000 gneg\n+band hsX q23 q23 110500000 116800000 gpos75\n+band hsX q24 q24 116800000 120700000 gneg\n+band hsX q25 q25 120700000 129800000 gpos100\n+band hsX q26.1 q26.1 129800000 130300000 gneg\n+band hsX q26.2 q26.2 130300000 133500000 gpos25\n+band hsX q26.3 q26.3 133500000 137800000 gneg\n+band hsX q27.1 q27.1 137800000 140100000 gpos75\n+band hsX q27.2 q27.2 140100000 141900000 gneg\n+band hsX q27.3 q27.3 141900000 146900000 gpos100\n+band hsX q28 q28 146900000 154913754 gneg\n+band hsY p11.32 p11.32 0 1700000 gneg\n+band hsY p11.31 p11.31 1700000 3300000 gpos50\n+band hsY p11.2 p11.2 3300000 11200000 gneg\n+band hsY p11.1 p11.1 11200000 11300000 acen\n+band hsY q11.1 q11.1 11300000 12500000 acen\n+band hsY q11.21 q11.21 12500000 14300000 gneg\n+band hsY q11.221 q11.221 14300000 19000000 gpos50\n+band hsY q11.222 q11.222 19000000 21300000 gneg\n+band hsY q11.223 q11.223 21300000 25400000 gpos50\n+band hsY q11.23 q11.23 25400000 27200000 gneg\n+band hsY q12 q12 27200000 57772954 gvar\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.human.hg19.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.human.hg19.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,886 @@\n+chr - hs1 1 0 249250621 chr1\n+chr - hs2 2 0 243199373 chr2\n+chr - hs3 3 0 198022430 chr3\n+chr - hs4 4 0 191154276 chr4\n+chr - hs5 5 0 180915260 chr5\n+chr - hs6 6 0 171115067 chr6\n+chr - hs7 7 0 159138663 chr7\n+chr - hs8 8 0 146364022 chr8\n+chr - hs9 9 0 141213431 chr9\n+chr - hs10 10 0 135534747 chr10\n+chr - hs11 11 0 135006516 chr11\n+chr - hs12 12 0 133851895 chr12\n+chr - hs13 13 0 115169878 chr13\n+chr - hs14 14 0 107349540 chr14\n+chr - hs15 15 0 102531392 chr15\n+chr - hs16 16 0 90354753 chr16\n+chr - hs17 17 0 81195210 chr17\n+chr - hs18 18 0 78077248 chr18\n+chr - hs19 19 0 59128983 chr19\n+chr - hs20 20 0 63025520 chr20\n+chr - hs21 21 0 48129895 chr21\n+chr - hs22 22 0 51304566 chr22\n+chr - hsX x 0 155270560 chrx\n+chr - hsY y 0 59373566 chry\n+band hs1 p36.33 p36.33 0 2300000 gneg\n+band hs1 p36.32 p36.32 2300000 5400000 gpos25\n+band hs1 p36.31 p36.31 5400000 7200000 gneg\n+band hs1 p36.23 p36.23 7200000 9200000 gpos25\n+band hs1 p36.22 p36.22 9200000 12700000 gneg\n+band hs1 p36.21 p36.21 12700000 16200000 gpos50\n+band hs1 p36.13 p36.13 16200000 20400000 gneg\n+band hs1 p36.12 p36.12 20400000 23900000 gpos25\n+band hs1 p36.11 p36.11 23900000 28000000 gneg\n+band hs1 p35.3 p35.3 28000000 30200000 gpos25\n+band hs1 p35.2 p35.2 30200000 32400000 gneg\n+band hs1 p35.1 p35.1 32400000 34600000 gpos25\n+band hs1 p34.3 p34.3 34600000 40100000 gneg\n+band hs1 p34.2 p34.2 40100000 44100000 gpos25\n+band hs1 p34.1 p34.1 44100000 46800000 gneg\n+band hs1 p33 p33 46800000 50700000 gpos75\n+band hs1 p32.3 p32.3 50700000 56100000 gneg\n+band hs1 p32.2 p32.2 56100000 59000000 gpos50\n+band hs1 p32.1 p32.1 59000000 61300000 gneg\n+band hs1 p31.3 p31.3 61300000 68900000 gpos50\n+band hs1 p31.2 p31.2 68900000 69700000 gneg\n+band hs1 p31.1 p31.1 69700000 84900000 gpos100\n+band hs1 p22.3 p22.3 84900000 88400000 gneg\n+band hs1 p22.2 p22.2 88400000 92000000 gpos75\n+band hs1 p22.1 p22.1 92000000 94700000 gneg\n+band hs1 p21.3 p21.3 94700000 99700000 gpos75\n+band hs1 p21.2 p21.2 99700000 102200000 gneg\n+band hs1 p21.1 p21.1 102200000 107200000 gpos100\n+band hs1 p13.3 p13.3 107200000 111800000 gneg\n+band hs1 p13.2 p13.2 111800000 116100000 gpos50\n+band hs1 p13.1 p13.1 116100000 117800000 gneg\n+band hs1 p12 p12 117800000 120600000 gpos50\n+band hs1 p11.2 p11.2 120600000 121500000 gneg\n+band hs1 p11.1 p11.1 121500000 125000000 acen\n+band hs1 q11 q11 125000000 128900000 acen\n+band hs1 q12 q12 128900000 142600000 gvar\n+band hs1 q21.1 q21.1 142600000 147000000 gneg\n+band hs1 q21.2 q21.2 147000000 150300000 gpos50\n+band hs1 q21.3 q21.3 150300000 155000000 gneg\n+band hs1 q22 q22 155000000 156500000 gpos50\n+band hs1 q23.1 q23.1 156500000 159100000 gneg\n+band hs1 q23.2 q23.2 159100000 160500000 gpos50\n+band hs1 q23.3 q23.3 160500000 165500000 gneg\n+band hs1 q24.1 q24.1 165500000 167200000 gpos50\n+band hs1 q24.2 q24.2 167200000 170900000 gneg\n+band hs1 q24.3 q24.3 170900000 172900000 gpos75\n+band hs1 q25.1 q25.1 172900000 176000000 gneg\n+band hs1 q25.2 q25.2 176000000 180300000 gpos50\n+band hs1 q25.3 q25.3 180300000 185800000 gneg\n+band hs1 q31.1 q31.1 185800000 190800000 gpos100\n+band hs1 q31.2 q31.2 190800000 193800000 gneg\n+band hs1 q31.3 q31.3 193800000 198700000 gpos100\n+band hs1 q32.1 q32.1 198700000 207200000 gneg\n+band hs1 q32.2 q32.2 207200000 211500000 gpos25\n+band hs1 q32.3 q32.3 211500000 214500000 gneg\n+band hs1 q41 q41 214500000 224100000 gpos100\n+band hs1 q42.11 q42.11 224100000 224600000 gneg\n+band hs1 q42.12 q42.12 224600000 227000000 gpos25\n+band hs1 q42.13 q42.13 227000000 230700000 gneg\n+band hs1 q42.2 q42.2 230700000 234700000 gpos50\n+band hs1 q42.3 q42.3 234700000 236600000 gneg\n+band hs1 q43 q43 236600000 243700000 gpos75\n+band hs1 q44 q44 243700000 249250621 gneg\n+band hs10 p15.3 p15.3 0 3000000 gneg\n+band hs10 p15.2 p15.2 3000000 3800000 gpos25\n+band hs10 p15.1 p15.1 3800000 6600000 gneg\n+band hs10 p14 p14 6600000 12200000 gpos75\n+band hs10 p13 p13 12200000 17300000 gneg\n+band hs10 p12.33 p12.33 17300000 18600000 gpos75\n+band hs10 p12.32 p'..b'band hs9 p21.2 p21.2 25600000 28000000 gneg\n+band hs9 p21.1 p21.1 28000000 33200000 gpos100\n+band hs9 p13.3 p13.3 33200000 36300000 gneg\n+band hs9 p13.2 p13.2 36300000 38400000 gpos25\n+band hs9 p13.1 p13.1 38400000 41000000 gneg\n+band hs9 p12 p12 41000000 43600000 gpos50\n+band hs9 p11.2 p11.2 43600000 47300000 gneg\n+band hs9 p11.1 p11.1 47300000 49000000 acen\n+band hs9 q11 q11 49000000 50700000 acen\n+band hs9 q12 q12 50700000 65900000 gvar\n+band hs9 q13 q13 65900000 68700000 gneg\n+band hs9 q21.11 q21.11 68700000 72200000 gpos25\n+band hs9 q21.12 q21.12 72200000 74000000 gneg\n+band hs9 q21.13 q21.13 74000000 79200000 gpos50\n+band hs9 q21.2 q21.2 79200000 81100000 gneg\n+band hs9 q21.31 q21.31 81100000 84100000 gpos50\n+band hs9 q21.32 q21.32 84100000 86900000 gneg\n+band hs9 q21.33 q21.33 86900000 90400000 gpos50\n+band hs9 q22.1 q22.1 90400000 91800000 gneg\n+band hs9 q22.2 q22.2 91800000 93900000 gpos25\n+band hs9 q22.31 q22.31 93900000 96600000 gneg\n+band hs9 q22.32 q22.32 96600000 99300000 gpos25\n+band hs9 q22.33 q22.33 99300000 102600000 gneg\n+band hs9 q31.1 q31.1 102600000 108200000 gpos100\n+band hs9 q31.2 q31.2 108200000 111300000 gneg\n+band hs9 q31.3 q31.3 111300000 114900000 gpos25\n+band hs9 q32 q32 114900000 117700000 gneg\n+band hs9 q33.1 q33.1 117700000 122500000 gpos75\n+band hs9 q33.2 q33.2 122500000 125800000 gneg\n+band hs9 q33.3 q33.3 125800000 130300000 gpos25\n+band hs9 q34.11 q34.11 130300000 133500000 gneg\n+band hs9 q34.12 q34.12 133500000 134000000 gpos25\n+band hs9 q34.13 q34.13 134000000 135900000 gneg\n+band hs9 q34.2 q34.2 135900000 137400000 gpos25\n+band hs9 q34.3 q34.3 137400000 141213431 gneg\n+band hsX p22.33 p22.33 0 4300000 gneg\n+band hsX p22.32 p22.32 4300000 6000000 gpos50\n+band hsX p22.31 p22.31 6000000 9500000 gneg\n+band hsX p22.2 p22.2 9500000 17100000 gpos50\n+band hsX p22.13 p22.13 17100000 19300000 gneg\n+band hsX p22.12 p22.12 19300000 21900000 gpos50\n+band hsX p22.11 p22.11 21900000 24900000 gneg\n+band hsX p21.3 p21.3 24900000 29300000 gpos100\n+band hsX p21.2 p21.2 29300000 31500000 gneg\n+band hsX p21.1 p21.1 31500000 37600000 gpos100\n+band hsX p11.4 p11.4 37600000 42400000 gneg\n+band hsX p11.3 p11.3 42400000 46400000 gpos75\n+band hsX p11.23 p11.23 46400000 49800000 gneg\n+band hsX p11.22 p11.22 49800000 54800000 gpos25\n+band hsX p11.21 p11.21 54800000 58100000 gneg\n+band hsX p11.1 p11.1 58100000 60600000 acen\n+band hsX q11.1 q11.1 60600000 63000000 acen\n+band hsX q11.2 q11.2 63000000 64600000 gneg\n+band hsX q12 q12 64600000 67800000 gpos50\n+band hsX q13.1 q13.1 67800000 71800000 gneg\n+band hsX q13.2 q13.2 71800000 73900000 gpos50\n+band hsX q13.3 q13.3 73900000 76000000 gneg\n+band hsX q21.1 q21.1 76000000 84600000 gpos100\n+band hsX q21.2 q21.2 84600000 86200000 gneg\n+band hsX q21.31 q21.31 86200000 91800000 gpos100\n+band hsX q21.32 q21.32 91800000 93500000 gneg\n+band hsX q21.33 q21.33 93500000 98300000 gpos75\n+band hsX q22.1 q22.1 98300000 102600000 gneg\n+band hsX q22.2 q22.2 102600000 103700000 gpos50\n+band hsX q22.3 q22.3 103700000 108700000 gneg\n+band hsX q23 q23 108700000 116500000 gpos75\n+band hsX q24 q24 116500000 120900000 gneg\n+band hsX q25 q25 120900000 128700000 gpos100\n+band hsX q26.1 q26.1 128700000 130400000 gneg\n+band hsX q26.2 q26.2 130400000 133600000 gpos25\n+band hsX q26.3 q26.3 133600000 138000000 gneg\n+band hsX q27.1 q27.1 138000000 140300000 gpos75\n+band hsX q27.2 q27.2 140300000 142100000 gneg\n+band hsX q27.3 q27.3 142100000 147100000 gpos100\n+band hsX q28 q28 147100000 155270560 gneg\n+band hsY p11.32 p11.32 0 2500000 gneg\n+band hsY p11.31 p11.31 2500000 3000000 gpos50\n+band hsY p11.2 p11.2 3000000 11600000 gneg\n+band hsY p11.1 p11.1 11600000 12500000 acen\n+band hsY q11.1 q11.1 12500000 13400000 acen\n+band hsY q11.21 q11.21 13400000 15100000 gneg\n+band hsY q11.221 q11.221 15100000 19800000 gpos50\n+band hsY q11.222 q11.222 19800000 22100000 gneg\n+band hsY q11.223 q11.223 22100000 26200000 gpos50\n+band hsY q11.23 q11.23 26200000 28800000 gneg\n+band hsY q12 q12 28800000 59373566 gvar\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.human.hg38.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.human.hg38.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,888 @@\n+chr - hs1 1 0 248956422 chr1\n+chr - hs2 2 0 242193529 chr2\n+chr - hs3 3 0 198295559 chr3\n+chr - hs4 4 0 190214555 chr4\n+chr - hs5 5 0 181538259 chr5\n+chr - hs6 6 0 170805979 chr6\n+chr - hs7 7 0 159345973 chr7\n+chr - hs8 8 0 145138636 chr8\n+chr - hs9 9 0 138394717 chr9\n+chr - hs10 10 0 133797422 chr10\n+chr - hs11 11 0 135086622 chr11\n+chr - hs12 12 0 133275309 chr12\n+chr - hs13 13 0 114364328 chr13\n+chr - hs14 14 0 107043718 chr14\n+chr - hs15 15 0 101991189 chr15\n+chr - hs16 16 0 90338345 chr16\n+chr - hs17 17 0 83257441 chr17\n+chr - hs18 18 0 80373285 chr18\n+chr - hs19 19 0 58617616 chr19\n+chr - hs20 20 0 64444167 chr20\n+chr - hs21 21 0 46709983 chr21\n+chr - hs22 22 0 50818468 chr22\n+chr - hsX X 0 156040895 chrx\n+chr - hsY Y 0 57227415 chry\n+#chr - hsM M 0 16569 chrm\n+band hs1 p36.33 p36.33 0 2300000 gneg\n+band hs1 p36.32 p36.32 2300000 5300000 gpos25\n+band hs1 p36.31 p36.31 5300000 7100000 gneg\n+band hs1 p36.23 p36.23 7100000 9100000 gpos25\n+band hs1 p36.22 p36.22 9100000 12500000 gneg\n+band hs1 p36.21 p36.21 12500000 15900000 gpos50\n+band hs1 p36.13 p36.13 15900000 20100000 gneg\n+band hs1 p36.12 p36.12 20100000 23600000 gpos25\n+band hs1 p36.11 p36.11 23600000 27600000 gneg\n+band hs1 p35.3 p35.3 27600000 29900000 gpos25\n+band hs1 p35.2 p35.2 29900000 32300000 gneg\n+band hs1 p35.1 p35.1 32300000 34300000 gpos25\n+band hs1 p34.3 p34.3 34300000 39600000 gneg\n+band hs1 p34.2 p34.2 39600000 43700000 gpos25\n+band hs1 p34.1 p34.1 43700000 46300000 gneg\n+band hs1 p33 p33 46300000 50200000 gpos75\n+band hs1 p32.3 p32.3 50200000 55600000 gneg\n+band hs1 p32.2 p32.2 55600000 58500000 gpos50\n+band hs1 p32.1 p32.1 58500000 60800000 gneg\n+band hs1 p31.3 p31.3 60800000 68500000 gpos50\n+band hs1 p31.2 p31.2 68500000 69300000 gneg\n+band hs1 p31.1 p31.1 69300000 84400000 gpos100\n+band hs1 p22.3 p22.3 84400000 87900000 gneg\n+band hs1 p22.2 p22.2 87900000 91500000 gpos75\n+band hs1 p22.1 p22.1 91500000 94300000 gneg\n+band hs1 p21.3 p21.3 94300000 99300000 gpos75\n+band hs1 p21.2 p21.2 99300000 101800000 gneg\n+band hs1 p21.1 p21.1 101800000 106700000 gpos100\n+band hs1 p13.3 p13.3 106700000 111200000 gneg\n+band hs1 p13.2 p13.2 111200000 115500000 gpos50\n+band hs1 p13.1 p13.1 115500000 117200000 gneg\n+band hs1 p12 p12 117200000 120400000 gpos50\n+band hs1 p11.2 p11.2 120400000 121700000 gneg\n+band hs1 p11.1 p11.1 121700000 123400000 acen\n+band hs1 q11 q11 123400000 125100000 acen\n+band hs1 q12 q12 125100000 143200000 gvar\n+band hs1 q21.1 q21.1 143200000 147500000 gneg\n+band hs1 q21.2 q21.2 147500000 150600000 gpos50\n+band hs1 q21.3 q21.3 150600000 155100000 gneg\n+band hs1 q22 q22 155100000 156600000 gpos50\n+band hs1 q23.1 q23.1 156600000 159100000 gneg\n+band hs1 q23.2 q23.2 159100000 160500000 gpos50\n+band hs1 q23.3 q23.3 160500000 165500000 gneg\n+band hs1 q24.1 q24.1 165500000 167200000 gpos50\n+band hs1 q24.2 q24.2 167200000 170900000 gneg\n+band hs1 q24.3 q24.3 170900000 173000000 gpos75\n+band hs1 q25.1 q25.1 173000000 176100000 gneg\n+band hs1 q25.2 q25.2 176100000 180300000 gpos50\n+band hs1 q25.3 q25.3 180300000 185800000 gneg\n+band hs1 q31.1 q31.1 185800000 190800000 gpos100\n+band hs1 q31.2 q31.2 190800000 193800000 gneg\n+band hs1 q31.3 q31.3 193800000 198700000 gpos100\n+band hs1 q32.1 q32.1 198700000 207100000 gneg\n+band hs1 q32.2 q32.2 207100000 211300000 gpos25\n+band hs1 q32.3 q32.3 211300000 214400000 gneg\n+band hs1 q41 q41 214400000 223900000 gpos100\n+band hs1 q42.11 q42.11 223900000 224400000 gneg\n+band hs1 q42.12 q42.12 224400000 226800000 gpos25\n+band hs1 q42.13 q42.13 226800000 230500000 gneg\n+band hs1 q42.2 q42.2 230500000 234600000 gpos50\n+band hs1 q42.3 q42.3 234600000 236400000 gneg\n+band hs1 q43 q43 236400000 243500000 gpos75\n+band hs1 q44 q44 243500000 248956422 gneg\n+band hs10 p15.3 p15.3 0 3000000 gneg\n+band hs10 p15.2 p15.2 3000000 3800000 gpos25\n+band hs10 p15.1 p15.1 3800000 6600000 gneg\n+band hs10 p14 p14 6600000 12200000 gpos75\n+band hs10 p13 p13 12200000 17300000 gneg\n+band hs10 p12.33 p12.33 17300000 18300000'..b'5600000 28000000 gneg\n+band hs9 p21.1 p21.1 28000000 33200000 gpos100\n+band hs9 p13.3 p13.3 33200000 36300000 gneg\n+band hs9 p13.2 p13.2 36300000 37900000 gpos25\n+band hs9 p13.1 p13.1 37900000 39000000 gneg\n+band hs9 p12 p12 39000000 40000000 gpos50\n+band hs9 p11.2 p11.2 40000000 42200000 gneg\n+band hs9 p11.1 p11.1 42200000 43000000 acen\n+band hs9 q11 q11 43000000 45500000 acen\n+band hs9 q12 q12 45500000 61500000 gvar\n+band hs9 q13 q13 61500000 65000000 gneg\n+band hs9 q21.11 q21.11 65000000 69300000 gpos25\n+band hs9 q21.12 q21.12 69300000 71300000 gneg\n+band hs9 q21.13 q21.13 71300000 76600000 gpos50\n+band hs9 q21.2 q21.2 76600000 78500000 gneg\n+band hs9 q21.31 q21.31 78500000 81500000 gpos50\n+band hs9 q21.32 q21.32 81500000 84300000 gneg\n+band hs9 q21.33 q21.33 84300000 87800000 gpos50\n+band hs9 q22.1 q22.1 87800000 89200000 gneg\n+band hs9 q22.2 q22.2 89200000 91200000 gpos25\n+band hs9 q22.31 q22.31 91200000 93900000 gneg\n+band hs9 q22.32 q22.32 93900000 96500000 gpos25\n+band hs9 q22.33 q22.33 96500000 99800000 gneg\n+band hs9 q31.1 q31.1 99800000 105400000 gpos100\n+band hs9 q31.2 q31.2 105400000 108500000 gneg\n+band hs9 q31.3 q31.3 108500000 112100000 gpos25\n+band hs9 q32 q32 112100000 114900000 gneg\n+band hs9 q33.1 q33.1 114900000 119800000 gpos75\n+band hs9 q33.2 q33.2 119800000 123100000 gneg\n+band hs9 q33.3 q33.3 123100000 127500000 gpos25\n+band hs9 q34.11 q34.11 127500000 130600000 gneg\n+band hs9 q34.12 q34.12 130600000 131100000 gpos25\n+band hs9 q34.13 q34.13 131100000 133100000 gneg\n+band hs9 q34.2 q34.2 133100000 134500000 gpos25\n+band hs9 q34.3 q34.3 134500000 138394717 gneg\n+#band hsM m m 0 16569 gneg\n+band hsX p22.33 p22.33 0 4400000 gneg\n+band hsX p22.32 p22.32 4400000 6100000 gpos50\n+band hsX p22.31 p22.31 6100000 9600000 gneg\n+band hsX p22.2 p22.2 9600000 17400000 gpos50\n+band hsX p22.13 p22.13 17400000 19200000 gneg\n+band hsX p22.12 p22.12 19200000 21900000 gpos50\n+band hsX p22.11 p22.11 21900000 24900000 gneg\n+band hsX p21.3 p21.3 24900000 29300000 gpos100\n+band hsX p21.2 p21.2 29300000 31500000 gneg\n+band hsX p21.1 p21.1 31500000 37800000 gpos100\n+band hsX p11.4 p11.4 37800000 42500000 gneg\n+band hsX p11.3 p11.3 42500000 47600000 gpos75\n+band hsX p11.23 p11.23 47600000 50100000 gneg\n+band hsX p11.22 p11.22 50100000 54800000 gpos25\n+band hsX p11.21 p11.21 54800000 58100000 gneg\n+band hsX p11.1 p11.1 58100000 61000000 acen\n+band hsX q11.1 q11.1 61000000 63800000 acen\n+band hsX q11.2 q11.2 63800000 65400000 gneg\n+band hsX q12 q12 65400000 68500000 gpos50\n+band hsX q13.1 q13.1 68500000 73000000 gneg\n+band hsX q13.2 q13.2 73000000 74700000 gpos50\n+band hsX q13.3 q13.3 74700000 76800000 gneg\n+band hsX q21.1 q21.1 76800000 85400000 gpos100\n+band hsX q21.2 q21.2 85400000 87000000 gneg\n+band hsX q21.31 q21.31 87000000 92700000 gpos100\n+band hsX q21.32 q21.32 92700000 94300000 gneg\n+band hsX q21.33 q21.33 94300000 99100000 gpos75\n+band hsX q22.1 q22.1 99100000 103300000 gneg\n+band hsX q22.2 q22.2 103300000 104500000 gpos50\n+band hsX q22.3 q22.3 104500000 109400000 gneg\n+band hsX q23 q23 109400000 117400000 gpos75\n+band hsX q24 q24 117400000 121800000 gneg\n+band hsX q25 q25 121800000 129500000 gpos100\n+band hsX q26.1 q26.1 129500000 131300000 gneg\n+band hsX q26.2 q26.2 131300000 134500000 gpos25\n+band hsX q26.3 q26.3 134500000 138900000 gneg\n+band hsX q27.1 q27.1 138900000 141200000 gpos75\n+band hsX q27.2 q27.2 141200000 143000000 gneg\n+band hsX q27.3 q27.3 143000000 148000000 gpos100\n+band hsX q28 q28 148000000 156040895 gneg\n+band hsY p11.32 p11.32 0 300000 gneg\n+band hsY p11.31 p11.31 300000 600000 gpos50\n+band hsY p11.2 p11.2 600000 10300000 gneg\n+band hsY p11.1 p11.1 10300000 10400000 acen\n+band hsY q11.1 q11.1 10400000 10600000 acen\n+band hsY q11.21 q11.21 10600000 12400000 gneg\n+band hsY q11.221 q11.221 12400000 17100000 gpos50\n+band hsY q11.222 q11.222 17100000 19600000 gneg\n+band hsY q11.223 q11.223 19600000 23800000 gpos50\n+band hsY q11.23 q11.23 23800000 26600000 gneg\n+band hsY q12 q12 26600000 57227415 gvar\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.mouse.mm10.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.mouse.mm10.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,424 @@\n+chr - mm1 1 0 195471971 chr1\n+chr - mm2 2 0 182113224 chr2\n+chr - mm3 3 0 160039680 chr3\n+chr - mm4 4 0 156508116 chr4\n+chr - mm5 5 0 151834684 chr5\n+chr - mm6 6 0 149736546 chr6\n+chr - mm7 7 0 145441459 chr7\n+chr - mm8 8 0 129401213 chr8\n+chr - mm9 9 0 124595110 chr9\n+chr - mm10 10 0 130694993 chr10\n+chr - mm11 11 0 122082543 chr11\n+chr - mm12 12 0 120129022 chr12\n+chr - mm13 13 0 120421639 chr13\n+chr - mm14 14 0 124902244 chr14\n+chr - mm15 15 0 104043685 chr15\n+chr - mm16 16 0 98207768 chr16\n+chr - mm17 17 0 94987271 chr17\n+chr - mm18 18 0 90702639 chr18\n+chr - mm19 19 0 61431566 chr19\n+chr - mmX x 0 171031299 chrx\n+chr - mmY y 0 91744698 chry\n+band mm1 qa1 qa1 0 8840440 gpos100\n+band mm1 qa2 qa2 8840440 12278390 gneg\n+band mm1 qa3 qa3 12278390 20136559 gpos33\n+band mm1 qa4 qa4 20136559 22101102 gneg\n+band mm1 qa5 qa5 22101102 30941543 gpos100\n+band mm1 qb qb 30941543 43219933 gneg\n+band mm1 qc1.1 qc1.1 43219933 54516052 gpos66\n+band mm1 qc1.2 qc1.2 54516052 55989459 gneg\n+band mm1 qc1.3 qc1.3 55989459 59427408 gpos75\n+band mm1 qc2 qc2 59427408 65321035 gneg\n+band mm1 qc3 qc3 65321035 74652612 gpos33\n+band mm1 qc4 qc4 74652612 80055103 gneg\n+band mm1 qc5 qc5 80055103 87422137 gpos33\n+band mm1 qd qd 87422137 99700527 gneg\n+band mm1 qe1.1 qe1.1 99700527 102647341 gpos33\n+band mm1 qe1.2 qe1.2 102647341 103629612 gneg\n+band mm1 qe2.1 qe2.1 103629612 112470053 gpos100\n+band mm1 qe2.2 qe2.2 112470053 113943460 gneg\n+band mm1 qe2.3 qe2.3 113943460 125730715 gpos100\n+band mm1 qe3 qe3 125730715 128677528 gneg\n+band mm1 qe4 qe4 128677528 139482511 gpos66\n+band mm1 qf qf 139482511 147340681 gneg\n+band mm1 qg1 qg1 147340681 151760902 gpos100\n+band mm1 qg2 qg2 151760902 152743173 gneg\n+band mm1 qg3 qg3 152743173 157163393 gpos100\n+band mm1 qh1 qh1 157163393 160110207 gneg\n+band mm1 qh2.1 qh2.1 160110207 164039292 gpos33\n+band mm1 qh2.2 qh2.2 164039292 165512699 gneg\n+band mm1 qh2.3 qh2.3 165512699 169932919 gpos33\n+band mm1 qh3 qh3 169932919 175826546 gneg\n+band mm1 qh4 qh4 175826546 181720174 gpos33\n+band mm1 qh5 qh5 181720174 188104936 gneg\n+band mm1 qh6 qh6 188104936 195471971 gpos33\n+band mm10 qa1 qa1 0 12822904 gpos100\n+band mm10 qa2 qa2 12822904 17754791 gneg\n+band mm10 qa3 qa3 17754791 23673055 gpos33\n+band mm10 qa4 qa4 23673055 33536828 gneg\n+band mm10 qb1 qb1 33536828 41427846 gpos100\n+band mm10 qb2 qb2 41427846 48332487 gneg\n+band mm10 qb3 qb3 48332487 56223506 gpos100\n+band mm10 qb4 qb4 56223506 64114524 gneg\n+band mm10 qb5.1 qb5.1 64114524 68060034 gpos100\n+band mm10 qb5.2 qb5.2 68060034 68553222 gneg\n+band mm10 qb5.3 qb5.3 68553222 74964675 gpos100\n+band mm10 qc1 qc1 74964675 89267146 gneg\n+band mm10 qc2 qc2 89267146 96171787 gpos33\n+band mm10 qc3 qc3 96171787 99130919 gneg\n+band mm10 qd1 qd1 99130919 111953824 gpos100\n+band mm10 qd2 qd2 111953824 124776729 gneg\n+band mm10 qd3 qd3 124776729 130694993 gpos33\n+band mm11 qa1 qa1 0 13046989 gpos100\n+band mm11 qa2 qa2 13046989 17240664 gneg\n+band mm11 qa3.1 qa3.1 17240664 21900303 gpos100\n+band mm11 qa3.2 qa3.2 21900303 25628014 gneg\n+band mm11 qa3.3 qa3.3 25628014 30287653 gpos100\n+band mm11 qa4 qa4 30287653 36345184 gneg\n+band mm11 qa5 qa5 36345184 43334643 gpos100\n+band mm11 qb1.1 qb1.1 43334643 47994282 gneg\n+band mm11 qb1.2 qb1.2 47994282 49858137 gpos33\n+band mm11 qb1.3 qb1.3 49858137 60109343 gneg\n+band mm11 qb2 qb2 60109343 62905127 gpos33\n+band mm11 qb3 qb3 62905127 70826513 gneg\n+band mm11 qb4 qb4 70826513 74088260 gpos33\n+band mm11 qb5 qb5 74088260 82009647 gneg\n+band mm11 qc qc 82009647 90396997 gpos100\n+band mm11 qd qd 90396997 102512059 gneg\n+band mm11 qe1 qe1 102512059 110433445 gpos66\n+band mm11 qe2 qe2 110433445 122082543 gneg\n+band mm12 qa1.1 qa1.1 0 17601321 gpos100\n+band mm12 qa1.2 qa1.2 17601321 21121586 gneg\n+band mm12 qa1.3 qa1.3 21121586 25961949 gpos66\n+band mm12 qa2 qa2 25961949 31682379 gneg\n+band mm12 qa3 qa3 31682379 39162941 gpos33\n+band mm12 qb1 qb1 39162941 44003304 gneg\n+band mm12 qb2 qb2 44003304 44883370 gpos33\n+band mm12 qb3'..b'pos33\n+band mm7 qb3 qb3 37500585 47635878 gneg\n+band mm7 qb4 qb4 47635878 54223819 gpos33\n+band mm7 qb5 qb5 54223819 60811759 gneg\n+band mm7 qc qc 60811759 71453817 gpos100\n+band mm7 qd1 qd1 71453817 77028229 gneg\n+band mm7 qd2 qd2 77028229 80575581 gpos66\n+band mm7 qd3 qd3 80575581 90204110 gneg\n+band mm7 qe1 qe1 90204110 99832639 gpos100\n+band mm7 qe2 qe2 99832639 102366462 gneg\n+band mm7 qe3 qe3 102366462 111488226 gpos33\n+band mm7 qf1 qf1 111488226 118582931 gneg\n+band mm7 qf2 qf2 118582931 123143813 gpos33\n+band mm7 qf3 qf3 123143813 137333224 gneg\n+band mm7 qf4 qf4 137333224 140880577 gpos33\n+band mm7 qf5 qf5 140880577 145441459 gneg\n+band mm8 qa1.1 qa1.1 0 15940729 gpos100\n+band mm8 qa1.2 qa1.2 15940729 16878419 gneg\n+band mm8 qa1.3 qa1.3 16878419 20160333 gpos33\n+band mm8 qa2 qa2 20160333 29537233 gneg\n+band mm8 qa3 qa3 29537233 33756838 gpos33\n+band mm8 qa4 qa4 33756838 44071427 gneg\n+band mm8 qb1.1 qb1.1 44071427 48291032 gpos66\n+band mm8 qb1.2 qb1.2 48291032 50166412 gneg\n+band mm8 qb1.3 qb1.3 50166412 55792551 gpos66\n+band mm8 qb2 qb2 55792551 59543311 gneg\n+band mm8 qb3.1 qb3.1 59543311 67044831 gpos100\n+band mm8 qb3.2 qb3.2 67044831 67982521 gneg\n+band mm8 qb3.3 qb3.3 67982521 74546350 gpos100\n+band mm8 qc1 qc1 74546350 80172490 gneg\n+band mm8 qc2 qc2 80172490 84860940 gpos33\n+band mm8 qc3 qc3 84860940 90018235 gneg\n+band mm8 qc4 qc4 90018235 91424770 gpos33\n+band mm8 qc5 qc5 91424770 95644374 gneg\n+band mm8 qd1 qd1 95644374 103145894 gpos100\n+band mm8 qd2 qd2 103145894 104083584 gneg\n+band mm8 qd3 qd3 104083584 110647414 gpos33\n+band mm8 qe1 qe1 110647414 123775073 gneg\n+band mm8 qe2 qe2 123775073 129401213 gpos33\n+band mm9 qa1 qa1 0 14412120 gpos100\n+band mm9 qa2 qa2 14412120 19526099 gneg\n+band mm9 qa3 qa3 19526099 24175170 gpos33\n+band mm9 qa4 qa4 24175170 38122384 gneg\n+band mm9 qa5.1 qa5.1 38122384 44166177 gpos66\n+band mm9 qa5.2 qa5.2 44166177 46490712 gneg\n+band mm9 qa5.3 qa5.3 46490712 54859040 gpos66\n+band mm9 qb qb 54859040 63227369 gneg\n+band mm9 qc qc 63227369 69736069 gpos33\n+band mm9 qd qd 69736069 77639490 gneg\n+band mm9 qe1 qe1 77639490 82753468 gpos33\n+band mm9 qe2 qe2 82753468 84613097 gneg\n+band mm9 qe3.1 qe3.1 84613097 91121796 gpos100\n+band mm9 qe3.2 qe3.2 91121796 91586703 gneg\n+band mm9 qe3.3 qe3.3 91586703 100884846 gpos100\n+band mm9 qe4 qe4 100884846 101814660 gpos66\n+band mm9 qf1 qf1 101814660 108323360 gneg\n+band mm9 qf2 qf2 108323360 111112803 gpos33\n+band mm9 qf3 qf3 111112803 119946038 gneg\n+band mm9 qf4 qf4 119946038 124595110 gpos33\n+band mmX qa1.1 qa1.1 0 15772338 gpos100\n+band mmX qa1.2 qa1.2 15772338 18236766 gneg\n+band mmX qa1.3 qa1.3 18236766 21194080 gpos33\n+band mmX qa2 qa2 21194080 28094478 gneg\n+band mmX qa3.1 qa3.1 28094478 33516219 gpos66\n+band mmX qa3.2 qa3.2 33516219 34501991 gneg\n+band mmX qa3.3 qa3.3 34501991 39923732 gpos66\n+band mmX qa4 qa4 39923732 47809902 gneg\n+band mmX qa5 qa5 47809902 56188957 gpos66\n+band mmX qa6 qa6 56188957 63089355 gneg\n+band mmX qa7.1 qa7.1 63089355 69496867 gpos66\n+band mmX qa7.2 qa7.2 69496867 70975524 gneg\n+band mmX qa7.3 qa7.3 70975524 77383037 gpos66\n+band mmX qb qb 77383037 82311893 gneg\n+band mmX qc1 qc1 82311893 91183833 gpos100\n+band mmX qc2 qc2 91183833 92169604 gneg\n+band mmX qc3 qc3 92169604 101041545 gpos100\n+band mmX qd qd 101041545 109913486 gneg\n+band mmX qe1 qe1 109913486 120264083 gpos100\n+band mmX qe2 qe2 120264083 121249854 gneg\n+band mmX qe3 qe3 121249854 135050651 gpos100\n+band mmX qf1 qf1 135050651 141458163 gneg\n+band mmX qf2 qf2 141458163 148851447 gpos33\n+band mmX qf3 qf3 148851447 156244731 gneg\n+band mmX qf4 qf4 156244731 163638015 gpos33\n+band mmX qf5 qf5 163638015 171031299 gneg\n+band mmY qa1 qa1 0 20642557 gpos100\n+band mmY qa2 qa2 20642557 32684048 gpos66\n+band mmY qb qb 32684048 45298944 gpos33\n+band mmY qc1 qc1 45298944 54473414 gpos100\n+band mmY qc2 qc2 54473414 61927671 gpos33\n+band mmY qc3 qc3 61927671 72248949 gpos100\n+band mmY qd qd 72248949 83143632 gpos33\n+band mmY qe qe 83143632 91744698 gpos66\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.mouse.mm9.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.mouse.mm9.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,424 @@\n+chr - mm1 1 0 197195432 chr1\n+chr - mm2 2 0 181748087 chr2\n+chr - mm3 3 0 159599783 chr3\n+chr - mm4 4 0 155630120 chr4\n+chr - mm5 5 0 152537259 chr5\n+chr - mm6 6 0 149517037 chr6\n+chr - mm7 7 0 152524553 chr7\n+chr - mm8 8 0 131738871 chr8\n+chr - mm9 9 0 124076172 chr9\n+chr - mm10 10 0 129993255 chr10\n+chr - mm11 11 0 121843856 chr11\n+chr - mm12 12 0 121257530 chr12\n+chr - mm13 13 0 120284312 chr13\n+chr - mm14 14 0 125194864 chr14\n+chr - mm15 15 0 103494974 chr15\n+chr - mm16 16 0 98319150 chr16\n+chr - mm17 17 0 95272651 chr17\n+chr - mm18 18 0 90772031 chr18\n+chr - mm19 19 0 61342430 chr19\n+chr - mmX x 0 166650296 chrx\n+chr - mmY y 0 15902555 chry\n+band mm1 qa1 qa1 0 8918386 gpos100\n+band mm1 qa2 qa2 8918386 12386647 gneg\n+band mm1 qa3 qa3 12386647 20314102 gpos33\n+band mm1 qa4 qa4 20314102 22295965 gneg\n+band mm1 qa5 qa5 22295965 31214352 gpos100\n+band mm1 qb qb 31214352 43601000 gneg\n+band mm1 qc1.1 qc1.1 43601000 54996715 gpos66\n+band mm1 qc1.2 qc1.2 54996715 56483113 gneg\n+band mm1 qc1.3 qc1.3 56483113 59951375 gpos75\n+band mm1 qc2 qc2 59951375 65896965 gneg\n+band mm1 qc3 qc3 65896965 75310818 gpos33\n+band mm1 qc4 qc4 75310818 80760943 gneg\n+band mm1 qc5 qc5 80760943 88192931 gpos33\n+band mm1 qd qd 88192931 100579579 gneg\n+band mm1 qe1.1 qe1.1 100579579 103552375 gpos33\n+band mm1 qe1.2 qe1.2 103552375 104543306 gneg\n+band mm1 qe2.1 qe2.1 104543306 113461693 gpos100\n+band mm1 qe2.2 qe2.2 113461693 114948091 gneg\n+band mm1 qe2.3 qe2.3 114948091 126839272 gpos100\n+band mm1 qe3 qe3 126839272 129812068 gneg\n+band mm1 qe4 qe4 129812068 140712318 gpos66\n+band mm1 qf qf 140712318 148639772 gneg\n+band mm1 qg1 qg1 148639772 153098966 gpos100\n+band mm1 qg2 qg2 153098966 154089897 gneg\n+band mm1 qg3 qg3 154089897 158549091 gpos100\n+band mm1 qh1 qh1 158549091 161521886 gneg\n+band mm1 qh2.1 qh2.1 161521886 165485613 gpos33\n+band mm1 qh2.2 qh2.2 165485613 166972011 gneg\n+band mm1 qh2.3 qh2.3 166972011 171431204 gpos33\n+band mm1 qh3 qh3 171431204 177376795 gneg\n+band mm1 qh4 qh4 177376795 183322386 gpos33\n+band mm1 qh5 qh5 183322386 189763443 gneg\n+band mm1 qh6 qh6 189763443 197195432 gpos33\n+band mm10 qa1 qa1 0 12754055 gpos100\n+band mm10 qa2 qa2 12754055 17659461 gneg\n+band mm10 qa3 qa3 17659461 23545948 gpos33\n+band mm10 qa4 qa4 23545948 33356759 gneg\n+band mm10 qb1 qb1 33356759 41205409 gpos100\n+band mm10 qb2 qb2 41205409 48072977 gneg\n+band mm10 qb3 qb3 48072977 55921626 gpos100\n+band mm10 qb4 qb4 55921626 63770276 gneg\n+band mm10 qb5.1 qb5.1 63770276 67694600 gpos100\n+band mm10 qb5.2 qb5.2 67694600 68185141 gneg\n+band mm10 qb5.3 qb5.3 68185141 74562168 gpos100\n+band mm10 qc1 qc1 74562168 88787845 gneg\n+band mm10 qc2 qc2 88787845 95655414 gpos33\n+band mm10 qc3 qc3 95655414 98598657 gneg\n+band mm10 qd1 qd1 98598657 111352712 gpos100\n+band mm10 qd2 qd2 111352712 124106767 gneg\n+band mm10 qd3 qd3 124106767 129993255 gpos33\n+band mm11 qa1 qa1 0 13021480 gpos100\n+band mm11 qa2 qa2 13021480 17206956 gneg\n+band mm11 qa3.1 qa3.1 17206956 21857485 gpos100\n+band mm11 qa3.2 qa3.2 21857485 25577908 gneg\n+band mm11 qa3.3 qa3.3 25577908 30228437 gpos100\n+band mm11 qa4 qa4 30228437 36274125 gneg\n+band mm11 qa5 qa5 36274125 43249918 gpos100\n+band mm11 qb1.1 qb1.1 43249918 47900447 gneg\n+band mm11 qb1.2 qb1.2 47900447 49760658 gpos33\n+band mm11 qb1.3 qb1.3 49760658 59991822 gneg\n+band mm11 qb2 qb2 59991822 62782139 gpos33\n+band mm11 qb3 qb3 62782139 70688038 gneg\n+band mm11 qb4 qb4 70688038 73943408 gpos33\n+band mm11 qb5 qb5 73943408 81849307 gneg\n+band mm11 qc qc 81849307 90220259 gpos100\n+band mm11 qd qd 90220259 102311634 gneg\n+band mm11 qe1 qe1 102311634 110217533 gpos66\n+band mm11 qe2 qe2 110217533 121843856 gneg\n+band mm12 qa1.1 qa1.1 0 17766671 gpos100\n+band mm12 qa1.2 qa1.2 17766671 21320005 gneg\n+band mm12 qa1.3 qa1.3 21320005 26205839 gpos66\n+band mm12 qa2 qa2 26205839 31980007 gneg\n+band mm12 qa3 qa3 31980007 39530843 gpos33\n+band mm12 qb1 qb1 39530843 44416677 gneg\n+band mm12 qb2 qb2 44416677 45305011 gpos33\n+band mm12 q'..b'326888 gpos33\n+band mm7 qb3 qb3 39326888 49955776 gneg\n+band mm7 qb4 qb4 49955776 56864554 gpos33\n+band mm7 qb5 qb5 56864554 63773332 gneg\n+band mm7 qc qc 63773332 74933665 gpos100\n+band mm7 qd1 qd1 74933665 80779554 gneg\n+band mm7 qd2 qd2 80779554 84499665 gpos66\n+band mm7 qd3 qd3 84499665 94597109 gneg\n+band mm7 qe1 qe1 94597109 104694553 gpos100\n+band mm7 qe2 qe2 104694553 107351775 gneg\n+band mm7 qe3 qe3 107351775 116917775 gpos33\n+band mm7 qf1 qf1 116917775 124357997 gneg\n+band mm7 qf2 qf2 124357997 129140997 gpos33\n+band mm7 qf3 qf3 129140997 144021442 gneg\n+band mm7 qf4 qf4 144021442 147741553 gpos33\n+band mm7 qf5 qf5 147741553 152524553 gneg\n+band mm8 qa1.1 qa1.1 0 16228701 gpos100\n+band mm8 qa1.2 qa1.2 16228701 17183331 gneg\n+band mm8 qa1.3 qa1.3 17183331 20524534 gpos33\n+band mm8 qa2 qa2 20524534 30070829 gneg\n+band mm8 qa3 qa3 30070829 34366662 gpos33\n+band mm8 qa4 qa4 34366662 44867586 gneg\n+band mm8 qb1.1 qb1.1 44867586 49163419 gpos66\n+band mm8 qb1.2 qb1.2 49163419 51072678 gneg\n+band mm8 qb1.3 qb1.3 51072678 56800455 gpos66\n+band mm8 qb2 qb2 56800455 60618973 gneg\n+band mm8 qb3.1 qb3.1 60618973 68256009 gpos100\n+band mm8 qb3.2 qb3.2 68256009 69210638 gneg\n+band mm8 qb3.3 qb3.3 69210638 75893045 gpos100\n+band mm8 qc1 qc1 75893045 81620822 gneg\n+band mm8 qc2 qc2 81620822 86393969 gpos33\n+band mm8 qc3 qc3 86393969 91644432 gneg\n+band mm8 qc4 qc4 91644432 93076376 gpos33\n+band mm8 qc5 qc5 93076376 97372209 gneg\n+band mm8 qd1 qd1 97372209 105009245 gpos100\n+band mm8 qd2 qd2 105009245 105963874 gneg\n+band mm8 qd3 qd3 105963874 112646281 gpos33\n+band mm8 qe1 qe1 112646281 126011094 gneg\n+band mm8 qe2 qe2 126011094 131738871 gpos33\n+band mm9 qa1 qa1 0 14352094 gpos100\n+band mm9 qa2 qa2 14352094 19444773 gneg\n+band mm9 qa3 qa3 19444773 24074481 gpos33\n+band mm9 qa4 qa4 24074481 37963604 gneg\n+band mm9 qa5.1 qa5.1 37963604 43982225 gpos66\n+band mm9 qa5.2 qa5.2 43982225 46297079 gneg\n+band mm9 qa5.3 qa5.3 46297079 54630553 gpos66\n+band mm9 qb qb 54630553 62964027 gneg\n+band mm9 qc qc 62964027 69445618 gpos33\n+band mm9 qd qd 69445618 77316122 gneg\n+band mm9 qe1 qe1 77316122 82408800 gpos33\n+band mm9 qe2 qe2 82408800 84260683 gneg\n+band mm9 qe3.1 qe3.1 84260683 90742275 gpos100\n+band mm9 qe3.2 qe3.2 90742275 91205245 gneg\n+band mm9 qe3.3 qe3.3 91205245 100464661 gpos100\n+band mm9 qe4 qe4 100464661 101390603 gpos66\n+band mm9 qf1 qf1 101390603 107872194 gneg\n+band mm9 qf2 qf2 107872194 110650019 gpos33\n+band mm9 qf3 qf3 110650019 119446464 gneg\n+band mm9 qf4 qf4 119446464 124076172 gpos33\n+band mmX qa1.1 qa1.1 0 15368327 gpos100\n+band mmX qa1.2 qa1.2 15368327 17769628 gneg\n+band mmX qa1.3 qa1.3 17769628 20651189 gpos33\n+band mmX qa2 qa2 20651189 27374832 gneg\n+band mmX qa3.1 qa3.1 27374832 32657694 gpos66\n+band mmX qa3.2 qa3.2 32657694 33618215 gneg\n+band mmX qa3.3 qa3.3 33618215 38901077 gpos66\n+band mmX qa4 qa4 38901077 46585241 gneg\n+band mmX qa5 qa5 46585241 54749664 gpos66\n+band mmX qa6 qa6 54749664 61473308 gneg\n+band mmX qa7.1 qa7.1 61473308 67716690 gpos66\n+band mmX qa7.2 qa7.2 67716690 69157471 gneg\n+band mmX qa7.3 qa7.3 69157471 75400854 gpos66\n+band mmX qb qb 75400854 80203456 gneg\n+band mmX qc1 qc1 80203456 88848140 gpos100\n+band mmX qc2 qc2 88848140 89808660 gneg\n+band mmX qc3 qc3 89808660 98453344 gpos100\n+band mmX qd qd 98453344 107098028 gneg\n+band mmX qe1 qe1 107098028 117183493 gpos100\n+band mmX qe2 qe2 117183493 118144013 gneg\n+band mmX qe3 qe3 118144013 131591300 gpos100\n+band mmX qf1 qf1 131591300 137834682 gneg\n+band mmX qf2 qf2 137834682 145038586 gpos33\n+band mmX qf3 qf3 145038586 152242489 gneg\n+band mmX qf4 qf4 152242489 159446392 gpos33\n+band mmX qf5 qf5 159446392 166650296 gneg\n+band mmY qa1 qa1 0 3578074 gpos100\n+band mmY qa2 qa2 3578074 5665285 gpos66\n+band mmY qb qb 5665285 7851886 gpos33\n+band mmY qc1 qc1 7851886 9442142 gpos100\n+band mmY qc2 qc2 9442142 10734224 gpos33\n+band mmY qc3 qc3 10734224 12523262 gpos100\n+band mmY qd qd 12523262 14411690 gpos33\n+band mmY qe qe 14411690 15902555 gpos66\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.oryzasativa.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.oryzasativa.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| @@ -0,0 +1,16 @@ +# Oryza sativa Msu Release 7 PlantGDB v187 22 Feb 2012 +# http://www.plantgdb.org/OsGDB/ +chr - os1 1 0 43270923 chr1 +chr - os2 2 0 35937250 chr2 +chr - os3 3 0 36413819 chr3 +chr - os4 4 0 35502694 chr4 +chr - os5 5 0 29958434 chr5 +chr - os6 6 0 31248787 chr6 +chr - os7 7 0 29697621 chr7 +chr - os8 8 0 28443022 chr8 +chr - os9 9 0 23012720 chr9 +chr - os10 10 0 23207287 chr10 +chr - os11 11 0 29021106 chr11 +chr - os12 12 0 27531856 chr12 +chr - os13 13 0 633585 chr13 +chr - os14 14 0 592136 chr14 |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.rat.rn4.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.rat.rn4.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -0,0 +1,267 @@\n+chr - rn1 1 0 267910886 chr1\n+chr - rn2 2 0 258207540 chr2\n+chr - rn3 3 0 171063335 chr3\n+chr - rn4 4 0 187126005 chr4\n+chr - rn5 5 0 173096209 chr5\n+chr - rn6 6 0 147636619 chr6\n+chr - rn7 7 0 143002779 chr7\n+chr - rn8 8 0 129041809 chr8\n+chr - rn9 9 0 113440463 chr9\n+chr - rn10 10 0 110718848 chr10\n+chr - rn11 11 0 87759784 chr11\n+chr - rn12 12 0 46782294 chr12\n+chr - rn13 13 0 111154910 chr13\n+chr - rn14 14 0 112194335 chr14\n+chr - rn15 15 0 109758846 chr15\n+chr - rn16 16 0 90238779 chr16\n+chr - rn17 17 0 97296363 chr17\n+chr - rn18 18 0 87265094 chr18\n+chr - rn19 19 0 59218465 chr19\n+chr - rn20 20 0 55268282 chr20\n+chr - rnX x 0 160699376 chrx\n+band rn1 p13 p13 0 10142096 gneg\n+band rn1 p12 p12 10142096 24272657 gvar\n+band rn1 p11 p11 24272657 38517175 gneg\n+band rn1 q11 q11 38517175 48659271 gpos\n+band rn1 q12 q12 48659271 69741157 gneg\n+band rn1 q21 q21 69741157 90025350 gpos\n+band rn1 q22 q22 90025350 123756368 gneg\n+band rn1 q31 q31 123756368 141191657 gpos\n+band rn1 q32 q32 141191657 162273543 gneg\n+band rn1 q33 q33 162273543 170478385 gpos\n+band rn1 q34 q34 170478385 174466850 gneg\n+band rn1 q35 q35 174466850 179822789 gpos\n+band rn1 q36 q36 179822789 187913675 gneg\n+band rn1 q37 q37 187913675 190762578 gpos\n+band rn1 q41 q41 190762578 204893140 gneg\n+band rn1 q42 q42 204893140 207400175 gpos\n+band rn1 q43 q43 207400175 223240078 gneg\n+band rn1 q51 q51 223240078 231330964 gpos\n+band rn1 q52 q52 231330964 239421850 gneg\n+band rn1 q53 q53 239421850 245575482 gpos\n+band rn1 q54 q54 245575482 253666368 gneg\n+band rn1 q55 q55 253666368 267910886 gvar\n+band rn10 q11 q11 0 6254774 gpos\n+band rn10 q12 q12 6254774 26232711 gneg\n+band rn10 q21 q21 26232711 34821357 gpos\n+band rn10 q22 q22 34821357 47517616 gneg\n+band rn10 q23 q23 47517616 49851488 gpos\n+band rn10 q24 q24 49851488 63761360 gneg\n+band rn10 q25 q25 63761360 66468650 gpos\n+band rn10 q26 q26 66468650 83085813 gneg\n+band rn10 q31 q31 83085813 88033620 gpos\n+band rn10 q32.1 q32.1 88033620 103717234 gneg\n+band rn10 q32.2 q32.2 103717234 105397621 gpos\n+band rn10 q32.3 q32.3 105397621 110718848 gneg\n+band rn11 p12 p12 0 6656992 gvar\n+band rn11 p11 p11 6656992 15001672 gneg\n+band rn11 q11 q11 15001672 36660337 gpos\n+band rn11 q12 q12 36660337 48380393 gneg\n+band rn11 q21 q21 48380393 64975993 gpos\n+band rn11 q22 q22 64975993 76696050 gneg\n+band rn11 q23 q23 76696050 87759784 gpos\n+band rn12 p12 p12 0 5483638 gvar\n+band rn12 p11 p11 5483638 12566672 gneg\n+band rn12 q11 q11 12566672 18678644 gpos\n+band rn12 q12 q12 18678644 26846981 gneg\n+band rn12 q13 q13 26846981 28446376 gpos\n+band rn12 q14 q14 28446376 32501984 gneg\n+band rn12 q15 q15 32501984 33930015 gpos\n+band rn12 q16 q16 33930015 46782294 gneg\n+band rn13 p13 p13 0 17399939 gneg\n+band rn13 p12 p12 17399939 22926979 gvar\n+band rn13 p11 p11 22926979 30194013 gneg\n+band rn13 q11 q11 30194013 40019861 gpos\n+band rn13 q12 q12 40019861 42988086 gneg\n+band rn13 q13 q13 42988086 55679807 gpos\n+band rn13 q21 q21 55679807 71749163 gpos\n+band rn13 q22 q22 71749163 80142075 gneg\n+band rn13 q23 q23 80142075 83007948 gpos\n+band rn13 q24 q24 83007948 91093802 gneg\n+band rn13 q25 q25 91093802 93959675 gpos\n+band rn13 q26 q26 93959675 105627870 gneg\n+band rn13 q27 q27 105627870 111154910 gpos\n+band rn14 p22 p22 0 21145501 gneg\n+band rn14 p21 p21 21145501 31410307 gpos\n+band rn14 p11 p11 31410307 49271071 gneg\n+band rn14 q11 q11 49271071 68671555 gpos\n+band rn14 q21 q21 68671555 94949460 gpos\n+band rn14 q22 q22 94949460 112194335 gneg\n+band rn15 p16 p16 0 14498477 gneg\n+band rn15 p15 p15 14498477 17183380 gpos\n+band rn15 p14 p14 17183380 31681858 gneg\n+band rn15 p13 p13 31681858 34366761 gneg\n+band rn15 p12 p12 34366761 47791278 gvar\n+band rn15 p11 p11 47791278 54235046 gneg\n+band rn15 q11 q11 54235046 60356625 gpos\n+band rn15 q12 q12 60356625 71848011 gneg\n+band rn15 q21 q21 71848011 86776073 gpos\n+band rn15 q22 q22 86776073 91716295 gneg\n+band rn15 q23 q23 91716295 99341421 gpos\n+band rn15 q24 q24 99341421 1062'..b'1 gpos\n+band rn3 q24 q24 60557821 78374833 gneg\n+band rn3 q31 q31 78374833 88284295 gpos\n+band rn3 q32 q32 88284295 91187067 gneg\n+band rn3 q33 q33 91187067 96191846 gpos\n+band rn3 q34 q34 96191846 99695191 gneg\n+band rn3 q35 q35 99695191 112207137 gpos\n+band rn3 q36 q36 112207137 128222429 gneg\n+band rn3 q41 q41 128222429 145338772 gneg\n+band rn3 q42 q42 145338772 165658174 gpos\n+band rn3 q43 q43 165658174 171063335 gneg\n+band rn4 q11 q11 0 15612157 gpos\n+band rn4 q12 q12 15612157 25397242 gneg\n+band rn4 q13 q13 25397242 31993929 gpos\n+band rn4 q21 q21 31993929 46176804 gpos\n+band rn4 q22 q22 46176804 69595041 gneg\n+band rn4 q23 q23 69595041 72343661 gpos\n+band rn4 q24 q24 72343661 92683444 gneg\n+band rn4 q31 q31 92683444 102908308 gpos\n+band rn4 q32 q32 102908308 104447535 gneg\n+band rn4 q33 q33 104447535 112253614 gpos\n+band rn4 q34 q34 112253614 136991188 gneg\n+band rn4 q41 q41 136991188 146776273 gneg\n+band rn4 q42 q42 146776273 170194509 gpos\n+band rn4 q43 q43 170194509 174152521 gneg\n+band rn4 q44 q44 174152521 187126005 gneg\n+band rn5 q11 q11 0 12292177 gpos\n+band rn5 q12 q12 12292177 20226219 gneg\n+band rn5 q13 q13 20226219 34529844 gpos\n+band rn5 q21 q21 34529844 51627145 gpos\n+band rn5 q22 q22 51627145 66824746 gneg\n+band rn5 q23 q23 66824746 69618423 gpos\n+band rn5 q24 q24 69618423 85486507 gneg\n+band rn5 q31 q31 85486507 104595256 gpos\n+band rn5 q32 q32 104595256 112194056 gneg\n+band rn5 q33 q33 112194056 123257016 gpos\n+band rn5 q34 q34 123257016 128509128 gneg\n+band rn5 q35 q35 128509128 135213952 gpos\n+band rn5 q36 q36 135213952 173096209 gneg\n+band rn6 q11 q11 0 3920547 gpos\n+band rn6 q12 q12 3920547 21058941 gneg\n+band rn6 q13 q13 21058941 25091504 gpos\n+band rn6 q14 q14 25091504 36629115 gneg\n+band rn6 q15 q15 36629115 40661678 gpos\n+band rn6 q16 q16 40661678 55783790 gneg\n+band rn6 q21 q21 55783790 67769464 gpos\n+band rn6 q22 q22 67769464 72138074 gneg\n+band rn6 q23 q23 72138074 83787701 gpos\n+band rn6 q24 q24 83787701 107647034 gneg\n+band rn6 q31 q31 107647034 119632707 gpos\n+band rn6 q32 q32 119632707 139571492 gneg\n+band rn6 q33 q33 139571492 147636619 gpos\n+band rn7 q11 q11 0 15273239 gpos\n+band rn7 q12 q12 15273239 18101617 gneg\n+band rn7 q13 q13 18101617 41068044 gpos\n+band rn7 q21 q21 41068044 52268420 gpos\n+band rn7 q22 q22 52268420 76479334 gneg\n+band rn7 q31 q31 76479334 91752574 gpos\n+band rn7 q32 q32 91752574 94580951 gneg\n+band rn7 q33 q33 94580951 104649976 gpos\n+band rn7 q34 q34 104649976 128860890 gneg\n+band rn7 q35 q35 128860890 136101537 gpos\n+band rn7 q36 q36 136101537 143002779 gneg\n+band rn8 q11 q11 0 11874368 gpos\n+band rn8 q12 q12 11874368 16813265 gneg\n+band rn8 q13 q13 16813265 31735037 gpos\n+band rn8 q21 q21 31735037 40351836 gpos\n+band rn8 q22 q22 40351836 48968634 gneg\n+band rn8 q23 q23 48968634 54222779 gpos\n+band rn8 q24 q24 54222779 82279915 gneg\n+band rn8 q31 q31 82279915 106554067 gpos\n+band rn8 q32 q32 106554067 129041809 gneg\n+band rn9 q11 q11 0 7255483 gpos\n+band rn9 q12 q12 7255483 17060190 gneg\n+band rn9 q13 q13 17060190 28237556 gpos\n+band rn9 q21 q21 28237556 41866100 gpos\n+band rn9 q22 q22 41866100 52357136 gneg\n+band rn9 q31 q31 52357136 62063796 gpos\n+band rn9 q32 q32 62063796 70103656 gneg\n+band rn9 q33 q33 70103656 78535705 gpos\n+band rn9 q34 q34 78535705 83732200 gneg\n+band rn9 q35 q35 83732200 90007212 gpos\n+band rn9 q36 q36 90007212 101184578 gneg\n+band rn9 q37 q37 101184578 107459591 gpos\n+band rn9 q38 q38 107459591 113440463 gneg\n+band rnX q11 q11 0 7738332 gpos\n+band rnX q12 q12 7738332 21538359 gneg\n+band rnX q13 q13 21538359 29792580 gpos\n+band rnX q14 q14 29792580 39465496 gneg\n+band rnX q21 q21 39465496 59585161 gpos\n+band rnX q22 q22 59585161 81252493 gneg\n+band rnX q31 q31 81252493 100985241 gpos\n+band rnX q32 q32 100985241 112463768 gneg\n+band rnX q33 q33 112463768 115688074 gpos\n+band rnX q34 q34 115688074 122523601 gneg\n+band rnX q35 q35 122523601 135420822 gpos\n+band rnX q36 q36 135420822 149220849 gneg\n+band rnX q37 q37 149220849 160699376 gpos\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.sorghum.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.sorghum.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| @@ -0,0 +1,14 @@ +# Sorghum bicolor Sbi1/Sbi1.4/SbGDB v181 23 Dec 2010 +# http://www.plantgdb.org/SbGDB/ +chr - sb1 1 0 73840631 chr1 +chr - sb2 2 0 77932606 chr2 +chr - sb3 3 0 74441160 chr3 +chr - sb4 4 0 68034345 chr4 +chr - sb5 5 0 62352331 chr5 +chr - sb6 6 0 62208784 chr6 +chr - sb7 7 0 64342021 chr7 +chr - sb8 8 0 55460251 chr8 +chr - sb9 9 0 59635592 chr9 +chr - sb10 10 0 60981646 chr10 +# chromosome 11 is composed of 88 unanchored scaffolds with 200 N spacing +chr - sb11 11 0 40203219 chr11 |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.yeast.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.yeast.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| @@ -0,0 +1,17 @@ +chr - chrI I 0 230218 chr1 +chr - chrII II 0 813184 chr2 +chr - chrIII III 0 316620 chr3 +chr - chrIV IV 0 1531933 chr4 +chr - chrV V 0 576874 chr5 +chr - chrVI VI 0 270161 chr6 +chr - chrVII VII 0 1090940 chr7 +chr - chrVIII VIII 0 562643 chr8 +chr - chrIX IX 0 439888 chr9 +chr - chrX X 0 745751 chr10 +chr - chrXI XI 0 666816 chr11 +chr - chrXII XII 0 1078177 chr12 +chr - chrXIII XIII 0 924431 chr13 +chr - chrXIV XIV 0 784333 chr14 +chr - chrXV XV 0 1091291 chr15 +chr - chrXVI XVI 0 948066 chr16 +chr - chrM M 0 85779 chrM |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d karyotype/karyotype.zeamays.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/karyotype/karyotype.zeamays.txt Fri May 01 07:28:50 2020 -0400 |
| b |
| @@ -0,0 +1,14 @@ +# Zea mays B73 RefGen v2 +# http://www.plantgdb.org/ZmGDB/ +chr - zm1 1 0 301354135 chr1 +chr - zm2 2 0 237068873 chr2 +chr - zm3 3 0 232140174 chr3 +chr - zm4 4 0 241473504 chr4 +chr - zm5 5 0 217872852 chr5 +chr - zm6 6 0 169174353 chr6 +chr - zm7 7 0 176764762 chr7 +chr - zm8 8 0 175793759 chr8 +chr - zm9 9 0 156750706 chr9 +chr - zm10 10 0 150189435 chr10 +# chromosome 11 is ChrUnkown - unanchored contigs with 100 n spacer +chr - zm11 11 0 7140151 chr11 |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d macros.xml --- a/macros.xml Thu Jan 23 07:27:22 2020 -0500 +++ b/macros.xml Fri May 01 07:28:50 2020 -0400 |
| b |
| b'@@ -2,7 +2,7 @@\n <macros>\n <token name="@CIRCOS_VERSION@">0.69.8</token>\n \n- <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy4</token>\n+ <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy5</token>\n \n <xml name="requirements">\n <requirements>\n@@ -12,6 +12,8 @@\n <requirement type="package" version="1.70">biopython</requirement>\n <requirement type="package" version="0.3.13">pybigwig</requirement>\n <requirement type="package" version="0.23">circos-tools</requirement>\n+ <requirement type="package" version="3.4">grep</requirement>\n+ <requirement type="package" version="5.1.0">gawk</requirement>\n <requirement type="package" version="1.29">tar</requirement>\n <yield />\n </requirements>\n@@ -80,6 +82,23 @@\n </param>\n </xml>\n \n+ <xml name="chrom_units"\n+ token_label="Position"\n+ token_help="In bases (e.g. 1000) or chromosome units (e.g. 1u)"\n+ token_value="5u"\n+ token_name="position"\n+ >\n+ <param name="@NAME@" type="text" value="@VALUE@" label="@LABEL@" help="@HELP@">\n+ <sanitizer>\n+ <valid initial="string.digits">\n+ <add value="u"/>\n+ <add value="b"/>\n+ <add value="."/>\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ </xml>\n+\n <xml name="circos_color_alpha"\n token_label="Color"\n token_name="color"\n@@ -93,13 +112,14 @@\n </valid>\n </sanitizer>\n </param>\n- <param name="@NAME@_alpha" type="float" label="Transparency" value="1" min="0" max="1" help="1 = fully opaque, 0 = fully transparent"/>\n+ <param name="@NAME@_alpha" type="float" label="@LABEL@ Transparency" value="1" min="0" max="1" help="1 = fully opaque, 0 = fully transparent"/>\n </xml>\n \n <xml name="brewer_scale"\n token_name="color"\n- token_label="Color">\n- <param name="@NAME@" type="select" label="@LABEL@">\n+ token_label="Color"\n+ token_help="">\n+ <param name="@NAME@" type="select" label="@LABEL@" help="@HELP@">\n <option value="purples-13-seq">Sequential: Purples</option>\n <option value="reds-13-seq">Sequential: Reds</option>\n <option value="oranges-13-seq">Sequential: Oranges</option>\n@@ -141,9 +161,11 @@\n </param>\n </xml>\n \n- <xml name="zdepth">\n- <param name="zdepth" type="float" value="" optional="true" label="Z-depth"\n- help="Optional. Datasets with a higher z-depth value are drawn on top of data sets with a lower value. Only useful if plotting multiple tracks"/>\n+ <xml name="zdepth"\n+ token_name="zdepth"\n+ >\n+ <param name="@NAME@" type="integer" value="0" optional="true" label="Z-index"\n+ help="Datasets with a higher z-index value are drawn on top of data sets with a lower value. 0 is the default and plots added lower in the configuration file will be plotted above."/>\n </xml>\n \n <xml name="font_select"\n@@ -161,26 +183,69 @@\n </param>\n </xml>\n \n+ <xml name="radial_position">\n+ <conditional name="radial_position">\n+ <param name="select" type="select" label="Radial Position">\n+ <option value="plot">Relative position</option>\n+ <option value="data" selected="True">Absolute position (values match data values)</option>\n+ </param>\n+ <when value="plot">\n+ <param name="y0" type="float" value="0" label="y0" help="Values are relative (0=inside of track, 1=outside of track)"/>\n+ <param name="y1" type="float" value="1" label="y1" help="Values are relative (0=inside of track, 1=outside of track)"/>\n+ </when>\n+ <when value="data">\n+ <param name="y0" type="float" value="0" label="y0" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y0 should be -10."/>\n+ <param name="y1" type="float" value="1" label="y1" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -'..b'>\n <option value="show">Change Visibility</option>\n- <option value="color">Change Link Color</option>\n+ <option value="z">Change Z-index</option>\n+ <option value="color">Change Fill Color</option>\n+ <option value="stroke_color">Change Stroke Color (Ribbons Only)</option>\n <option value="thickness">Change Thickness</option>\n- <option value="z">Change Z-depth</option>\n </param>\n <when value="show">\n <param name="action_value" type="boolean" label="Show" truevalue="yes" falsevalue="no"/>\n </when>\n+ <when value="stroke_color">\n+ <expand macro="link_color_action_options" section="Stroke"/>\n+ </when>\n <when value="color">\n- <conditional name="dynamic">\n- <param name="dynamic_select" type="select" label="Static / Dynamic Change">\n- <option value="static">Static: Change is always applied</option>\n- <option value="dynamic">Dynamic: Change is sometimes applied</option>\n- </param>\n- <when value="static">\n- <expand macro="circos_color_alpha" label="Link Color" name="action_value"/>\n- </when>\n- <when value="dynamic">\n- <expand macro="brewer_scale" label="Fill Color" name="action_value"/>\n- <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>\n- <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>\n- <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />\n- </when>\n- </conditional>\n+ <expand macro="link_color_action_options" section="Fill"/>\n </when>\n <when value="thickness">\n <param name="action_value" type="integer" value="1" label="Thickness"/>\n </when>\n <when value="z">\n <conditional name="dynamic">\n- <param name="dynamic_select" type="select" label="Static or Dynamic Z-Depth">\n+ <param name="dynamic_select" type="select" label="Static or Dynamic Z-Index">\n <option value="static">Static</option>\n <option value="dynamic">Dynamic (based on value)</option>\n </param>\n <when value="static">\n- <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"/>\n+ <expand macro="zdepth" name="action_value"/>\n </when>\n <when value="dynamic">\n <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>\n <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>\n- <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Z-Depth Mapping" />\n+ <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Z-Index Mapping" />\n </when>\n </conditional>\n </when>\n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d macros_conffiles.xml --- a/macros_conffiles.xml Thu Jan 23 07:27:22 2020 -0500 +++ b/macros_conffiles.xml Fri May 01 07:28:50 2020 -0400 |
| [ |
| b'@@ -7,6 +7,11 @@\n <<include colors_fonts_patterns.conf>>\n <<include housekeeping.conf>>\n \n+max_ticks* = ${limits.max_ticks}\n+max_ideograms* = ${limits.max_ideograms}\n+max_links* = ${limits.max_links}\n+max_points_per_track* = ${limits.max_points_per_track}\n+\n <colors>\n <<include karyotype-colors.conf>>\n \n@@ -50,7 +55,8 @@\n svg = yes\n #end if\n # by default angle = 0 is at 3 o\'clock position\n- angle_offset = -90\n+ angle_offset = ${ideogram.angle_offset}\n+ angle_orientation = ${ideogram.angle_orientation}\n auto_alpha_colors = yes\n auto_alpha_steps = 5\n #if str($plot_options.background.background_select) == \'transparent\':\n@@ -61,10 +67,20 @@\n radius* = ${plot_options.radius}p\n </image>\n \n+<zooms>\n+ #for zoom in $scaling.zooms:\n+ <zoom>\n+ chr = ${zoom.chr}\n+ start = ${zoom.start}u\n+ end = ${zoom.end}u\n+ scale = ${zoom.scale}\n+ </zoom>\n+ #end for\n+</zooms>\n+\n <<include ticks.conf>>\n <<include ideogram.conf>>\n <<include data.conf>>\n-<<include highlight.conf>>\n <<include links.conf>>\n \n ]]></configfile>\n@@ -73,7 +89,7 @@\n <configfile name="ticks_conf"><![CDATA[\n @UTILS@\n \n-show_ticks = ${ticks.show_ticks}\n+show_ticks = yes\n show_tick_labels = yes\n \n \n@@ -97,7 +113,7 @@\n \n #for $tick_group in $ticks.tick_group:\n <tick>\n- spacing = ${tick_group.spacing}\n+ spacing = ${tick_group.spacing}u\n size = ${tick_group.size}p\n show_label = ${tick_group.ticks.show_tick_labels}\n color = $circosColor($tick_group.color)\n@@ -131,7 +147,13 @@\n <ideogram>\n <spacing>\n ## spacing between ideograms\n- default = ${ideogram.spacing}r\n+ default = ${ideogram.spacing}u\n+\n+ #for pairwise in $ideogram.pairwise_spacing\n+ <pairwise ${pairwise.chr1} ${pairwise.chr2}>\n+ spacing = ${pairwise.spacing}u\n+ </pairwise>\n+ #end for\n </spacing>\n \n # ideogram position, thickness and fill\n@@ -143,7 +165,7 @@\n label_size = ${ideogram.ideogram_labels.size}\n label_parallel = ${ideogram.ideogram_labels.parallel}\n \n- #if $ideogram.bands.bands:\n+ #if $ideogram.bands.show_bands:\n show_bands = yes\n #else\n show_bands = no\n@@ -157,77 +179,6 @@\n </ideogram>\n ]]></configfile>\n </xml>\n- <xml name="configfile_highlight_conf">\n- <configfile name="highlight_conf"><![CDATA[\n-@UTILS@\n-<highlights>\n-#for $hi, $data in enumerate($sec_highlight.data):\n- <highlight>\n- file = data/highlight-${hi}.txt # ${data.data_source.element_identifier}\n- r1 = ${data.r1}r\n- r0 = ${data.r0}r\n- fill_color = $circosColorAlpha($data.fill_color, $data.fill_color_alpha)\n- stroke_color = $circosColorAlpha($data.stroke_color, $data.stroke_color_alpha)\n- stroke_thickness = ${data.stroke_thickness}\n-\n- <rules>\n- #for $rule in $data.sec_rule.rules:\n- <rule>\n- #for $condition in $rule.conditions\n- #if str($condition.application.application_select) == "1":\n- condition = 1\n- #elif str($condition.application.application_select) == "on":\n- condition = on($condition.application.on_genomes)\n- #elif str($condition.application.application_select) == "pos":\n- #if $condition.application.pos_gt:\n- condition = var(start) > $condition.application.pos_gt\n- #end if\n-\n- #if $condition.application.pos_lt:\n- #if $condition.application.pos_lt_sub == \'yes\':\n- condition = var(end) < chrlen(var(chr)) - $condition.application.pos_lt\n- #else\n- condition = var(end) < $condition.application.pos_lt\n- #end if\n- #end if\n- '..b'- #elif $cond == \'always\'\n+ #if $cond == \'always\'\n condition = 1\n #elif $cond == \'random\'\n condition = rand() < ${condition.application.value}\n+ #elif $cond == \'interchr\' or $cond == \'intrachr\' or $cond == \'inv\' or $cond == \'rev\'\n+ condition = var($cond)\n #else\n #set op = $condition.application.comparison.compare\n #set val = $condition.application.comparison.compval\n #if $cond == \'chr\'\n #if $op == \'between\' or $op == \'fromto\'\n #set val2 = $condition.application.comparison.compval2\n- #set c=\'\'.join([str($op),"(",str($val),",",str($val2),")"])\n+ condition = ${op}(${val}, ${val2})\n #elif $op == \'on\'\n- #set c=\'(var(chr1) eq "%s" or var(chr2) eq "%s")\' % (str($val), str($val))\n+ condition = var(chr1) eq "${val}" or var(chr2) eq "${val}"\n #else\n- #set c=\'\'.join([str($op),"(",str($val),")"])\n+ condition = ${op}(${val})\n #end if\n- condition = $c\n #else\n #if $cond == \'dist\' and $op == \'lt\'\n condition = abs(var(pos1) - var(pos2)) < $val\n@@ -481,30 +469,27 @@\n \n #for $action in $rule.actions:\n #set actiontype = $action.action.action_select\n- #if $actiontype == \'color\':\n+ #if $actiontype in (\'color\', \'stroke_color\'):\n #if $action.action.dynamic.dynamic_select == "static":\n #set actionval = $circosColorAlpha($action.action.dynamic.action_value, $action.action.dynamic.action_value_alpha)\n $actiontype = $actionval\n- #else\n- #set x_fill_color = $action.action.dynamic.action_value\n- #set x_fill_color_count = int(str($x_fill_color).split(\'-\')[1])\n- #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1\n- #set x_max = 1 if $action.action.dynamic.invert else $x_fill_color_count\n-\n- $actiontype = eval(sprintf("${action.action.dynamic.action_value}-%d", remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max})))\n+ #elif $action.action.dynamic.dynamic_select == \'source\':\n+ $actiontype = eval(var(chr1))\n+ #elif $action.action.dynamic.dynamic_select == \'dest\':\n+ $actiontype = eval(var(chr2))\n #end if\n #elif $actiontype == \'z\':\n #if $action.action.dynamic.dynamic_select == "static":\n- #set actionval = $action.action.dynamic.action_value\n- $actiontype = $actionval\n+ $actiontype = ${action.action.dynamic.action_value}\n #else\n #set x_min = 1000 if $action.action.dynamic.invert else 1\n #set x_max = 1 if $action.action.dynamic.invert else 1000\n $actiontype = eval(remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max}))\n #end if\n+ #elif $actiontype == \'value_from_attr\':\n+ value = var(${action.action.action_value})\n #else\n- #set actionval = $action.action.action_value\n- $actiontype = $actionval\n+ $actiontype = ${action.action.action_value}\n #end if\n #end for\n \n' |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d macros_tests.xml --- a/macros_tests.xml Thu Jan 23 07:27:22 2020 -0500 +++ b/macros_tests.xml Fri May 01 07:28:50 2020 -0400 |
| b |
| @@ -30,14 +30,16 @@ <param name="svg" value="yes" /> </section> - <section name="ticks"> - <param name="show_ticks" value="yes" /> + <section name="ideogram"> + <param name="units" value="kb" /> + </section> + <section name="ticks"> <repeat name="tick_group"> - <param name="spacing" value="5000" /> + <param name="spacing" value="1" /> </repeat> <repeat name="tick_group"> - <param name="spacing" value="20000" /> + <param name="spacing" value="5" /> <conditional name="ticks"> <param name="show_tick_labels" value="yes" /> <param name="format" value="%.1f" /> |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d stack-histogram.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stack-histogram.py Fri May 01 07:28:50 2020 -0400 |
| [ |
| @@ -0,0 +1,27 @@ +#!/usr/bin/env python +import logging +import sys + +import pyBigWig + +logging.basicConfig(level=logging.INFO) +log = logging.getLogger() + +if __name__ == "__main__": + files = sys.argv[1:] + bws = [pyBigWig.open(x) for x in files] + + # obtain some chroms. Hope all sets are identical! + k = bws[0].chroms().keys() + + # do magic? + # nah. + # just assert that intervals are identical. + # and crash otherwise. + # sorry not sorry. + + for chrom in k: + for interval_set in zip(*[bw.intervals(chrom) for bw in bws]): + (start, end) = interval_set[0][0:2] + values = ','.join(map(str, [x[2] for x in interval_set])) + sys.stdout.write("%s\t%s\t%s\t%s\n" % (chrom, start, end, values)) |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d stack-histogram.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stack-histogram.xml Fri May 01 07:28:50 2020 -0400 |
| [ |
| @@ -0,0 +1,35 @@ +<?xml version="1.0"?> +<tool id="circos_wiggle_to_stacked" name="Circos: Stack bigWigs as Histogram" version="@WRAPPER_VERSION@"> + <description>reformats for use in Circos stacked histogram plots</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + </expand> + <command detect_errors="exit_code"><![CDATA[ +python + '$__tool_directory__/stack-histogram.py' + #for i in $input + '$i' + #end for + > '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="bigwig" label="BigWig files" multiple="True" help="These MUST have identical chromosomes and intervals, within their datasets. This tool is incredibly, intentionally naïve, and will crash if there are missing ranges in some bigwig files. This feels like a reasonable assumption to make (simplifies processing) at the expense of theoretical correctness, given that when you are stacking histograms they're probably coming from the same upstream pipeline with the same settings (i.e. step/width/etc.)"/> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <tests> + <test> + <param name="input" value="scatter/1.bw,scatter/1.bw,scatter/1.bw" ftype="bigwig" /> + <output name="output" file="scatter/1.multi.out" ftype="tabular" /> + </test> + </tests> + <help><![CDATA[ +Converts standard bigWig files into a format appropriate for Circos stacked histogram plots + +If you need to process bedgraph, please convert those to bigwig first. + ]]></help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d test-data/0/out.png |
| b |
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-NC_000913.3 28373 29195 name=dapB,strand=1,value=0 -NC_000913.3 29650 30799 name=carA,strand=1,value=0 -NC_000913.3 30816 34038 name=carB,strand=1,value=0 -NC_000913.3 34299 34695 name=caiF,strand=1,value=0 -NC_000913.3 34727 34763 name=None,strand=1,value=0 -NC_000913.3 34780 35371 name=caiE,strand=-1,value=0 -NC_000913.3 35376 36162 name=caiD,strand=-1,value=0 -NC_000913.3 36270 37824 name=caiC,strand=-1,value=0 -NC_000913.3 37897 39115 name=caiB,strand=-1,value=0 -NC_000913.3 39151 39185 name=None,strand=1,value=0 -NC_000913.3 39197 39233 name=None,strand=-1,value=0 -NC_000913.3 39243 40386 name=caiA,strand=-1,value=0 -NC_000913.3 40416 41931 name=caiT,strand=-1,value=0 +NC_000913.3 0 4641652 name=ANONYMOUS,strand=1,type=region,value=0 +NC_000913.3 189 255 name=thrL,strand=1,type=gene,value=0 +NC_000913.3 336 2799 name=thrA,strand=1,type=gene,value=0 +NC_000913.3 2800 3733 name=thrB,strand=1,type=gene,value=0 +NC_000913.3 3733 5020 name=thrC,strand=1,type=gene,value=0 +NC_000913.3 5233 5530 name=yaaX,strand=1,type=gene,value=0 +NC_000913.3 5565 5601 name=None,strand=1,type=repeat_region,value=0 +NC_000913.3 5636 5670 name=None,strand=-1,type=repeat_region,value=0 +NC_000913.3 5682 6459 name=yaaA,strand=-1,type=gene,value=0 +NC_000913.3 6528 7959 name=yaaJ,strand=-1,type=gene,value=0 +NC_000913.3 8237 9191 name=talB,strand=1,type=gene,value=0 +NC_000913.3 9305 9893 name=mog,strand=1,type=gene,value=0 +NC_000913.3 9927 10494 name=satP,strand=-1,type=gene,value=0 +NC_000913.3 10642 11356 name=yaaW,strand=-1,type=gene,value=0 +NC_000913.3 10829 11315 name=mbiA,strand=1,type=gene,value=0 +NC_000913.3 11381 11786 name=yaaI,strand=-1,type=gene,value=0 +NC_000913.3 12162 14079 name=dnaK,strand=1,type=gene,value=0 +NC_000913.3 14167 15298 name=dnaJ,strand=1,type=gene,value=0 +NC_000913.3 15386 16731 name=None,strand=1,type=mobile_genetic_element,value=0 +NC_000913.3 15444 16557 name=insL-1,strand=1,type=gene,value=0 +NC_000913.3 16750 16960 name=mokC,strand=-1,type=gene,value=0 +NC_000913.3 16750 16903 name=hokC,strand=-1,type=gene,value=0 +NC_000913.3 16951 17006 name=sokC,strand=1,type=gene,value=0 +NC_000913.3 17488 18655 name=nhaA,strand=1,type=gene,value=0 +NC_000913.3 18714 19620 name=nhaR,strand=1,type=gene,value=0 +NC_000913.3 19795 20563 name=None,strand=-1,type=mobile_genetic_element,value=0 +NC_000913.3 19810 20314 name=insB-1,strand=-1,type=gene,value=0 +NC_000913.3 20232 20508 name=insA-1,strand=-1,type=gene,value=0 +NC_000913.3 20814 21078 name=rpsT,strand=-1,type=gene,value=0 +NC_000913.3 21180 21399 name=yaaY,strand=1,type=gene,value=0 +NC_000913.3 21406 22348 name=ribF,strand=1,type=gene,value=0 +NC_000913.3 22390 25207 name=ileS,strand=1,type=gene,value=0 +NC_000913.3 25206 25701 name=lspA,strand=1,type=gene,value=0 +NC_000913.3 25710 25746 name=None,strand=1,type=repeat_region,value=0 +NC_000913.3 25762 25796 name=None,strand=-1,type=repeat_region,value=0 +NC_000913.3 25825 26275 name=fkpB,strand=1,type=gene,value=0 +NC_000913.3 26276 27227 name=ispH,strand=1,type=gene,value=0 +NC_000913.3 27292 28207 name=rihC,strand=1,type=gene,value=0 +NC_000913.3 28373 29195 name=dapB,strand=1,type=gene,value=0 +NC_000913.3 29650 30799 name=carA,strand=1,type=gene,value=0 +NC_000913.3 30816 34038 name=carB,strand=1,type=gene,value=0 +NC_000913.3 34299 34695 name=caiF,strand=1,type=gene,value=0 +NC_000913.3 34727 34763 name=None,strand=1,type=repeat_region,value=0 +NC_000913.3 34780 35371 name=caiE,strand=-1,type=gene,value=0 +NC_000913.3 35376 36162 name=caiD,strand=-1,type=gene,value=0 +NC_000913.3 36270 37824 name=caiC,strand=-1,type=gene,value=0 +NC_000913.3 37897 39115 name=caiB,strand=-1,type=gene,value=0 +NC_000913.3 39151 39185 name=None,strand=1,type=repeat_region,value=0 +NC_000913.3 39197 39233 name=None,strand=-1,type=repeat_region,value=0 +NC_000913.3 39243 40386 name=caiA,strand=-1,type=gene,value=0 +NC_000913.3 40416 41931 name=caiT,strand=-1,type=gene,value=0 |
| b |
| diff -r a64dc31ab7f2 -r 740057a5126d tiles-from-gff3.py --- a/tiles-from-gff3.py Thu Jan 23 07:27:22 2020 -0500 +++ b/tiles-from-gff3.py Fri May 01 07:28:50 2020 -0400 |
| [ |
| @@ -24,6 +24,7 @@ "strand": 0 if not feature.location.strand else feature.location.strand, "name": feature.qualifiers.get(attr, ["None"])[0] or feature.id, "value": feature.qualifiers.get("score", [0])[0], + "type": feature.type, } line = [ |
