Package: tagore
tagoreInstallationRequirementsQuick startUsageInput file descriptionEtymologytagoretagoreis a simple way to visualize features on human chromosome ideograms as shown in this article:https://www.nature.com/articles/srep12376tagorewas designed to allow everyone to create 23andMe style chromosome painting diagrams.Installationtagoreis a simple Python script that uses the RSVG library and has no other depenendies.pipinstalltagore
tagore--version# tagore (version 1.1.2)RequirementsPython 3.6+RSVGClick(automatically installed ifpipis used)Quick startThe demo data consists ofCatalogue of Somatic Mutations in Cancer (COSMIC) Cancer Gene Censusgenes and 100 randomly simulated mutations.  Points represent single nucleotide variants (i.e. variant present in <3 samples); triangles represent single nucleotide polymorphisms (i.e. variants found in many samples); and short lines (single chromosome) represent known INDEL sites.tagore--inputexample_ideogram/test.bed--prefixexample_ideogram/example-vfUsageusage: tagore [-h] [--version] -i <input.bed> [-p [output file prefix]] [-b [hg78/hg38]] [-f] [-v]

tagore: a utility for illustrating human chromosomes https://github.com/jordanlab/tagore

optional arguments:
  -h, --help                                              show this help message and exit
  --version                                               Print the software version
  -i <input.bed>, --input <input.bed>                     Input BED-like file
  -p [output file prefix], --prefix [output file prefix]  Output prefix [Default: "out"]
  -b [hg78/hg38], --build [hg78/hg38]                     Human genome build to use [Default: hg38]
  -f, --force                                             Overwrite output files if they exist already
  -v, --verbose                                           Display verbose outputThe input file is a bed-like format, described below.  If an output prefix is not specified, the scripts uses "out" as the default prefix.Helper scripts for converting RFMix and ADMIXTURE outputs are included in thescripts/folder.A more complete example of a full chromosome painting using an RFMix output can be seen by running:rfmix2tagore--chr1example_ideogram/1KGP-MXL104_chr1.bed\--chr2example_ideogram/1KGP-MXL104_chr2.bed\--outexample_ideogram/1KGP-MXL104_tagore.bed

tagore--inputexample_ideogram/1KGP-MXL104_tagore.bed\--prefixexample_ideogram/1KGP-MXL104\--buildhg37\--verboseInput file description#chr	start	stop	feature	size	color	chrCopy
chr1	10000000	20000000	0	1	#FF0000	1
chr2	20000000	30000000	0	1	#FF0000	2
chr2	40000000	50000000	0	0.5	#FF0000	1Each column is explained below:chr- The chromosome on which a feature has to be drawnstart- Start position (in bp) for featurestop- Stop position (in bp) for featurefeature- The shape of the feature to be drawn0 will draw a rectangle1 will draw a circle2 will draw a triangle pointing to the genomic location3 will draw a line at that genomic locationsize- The horizontal size of the feature. Should range between 0 and 1.color- Specify the color of the genomic feature with a hex value (#FF0000 for red, etc.)chrCopy- Specify the chromosome copy on which the feature should be drawn (1 or 2).  To draw the same feature on both chromosomes, you must specify the feature twiceEtymologyTagore(/tæˈgɔːr/) was a prolific songwriter,
artist, and influential poet of 19th and 20th century India.  Notably, Tagore spoke out against
racial prejudice and espoused the princple respect for all people, regardless of ancestry or
ethnic bacground.