Skip to main content
Join the official 2019 Python Developers SurveyStart the survey!

A simple way to visualize features on human chromosome ideograms

Project description

tagore

tagore is a simple way to visualize features on human chromosome ideograms as shown in this article: https://www.nature.com/articles/srep12376

tagore was designed to allow everyone to create 23andMe style chromosome painting diagrams.

tagore

Installation

tagore is a simple Python script that uses the RSVG library and has no other depenendies.

pip install tagore
tagore --version
# tagore (version 1.0.1)

Requirements

  • Python 3.6+
  • RSVG
  • Click (automatically installed if pip is used)

Quick start

The demo data consists of Catalogue of Somatic Mutations in Cancer (COSMIC) Cancer Gene Census genes 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 --input example_ideogram/test.bed --prefix example_ideogram/example -vf

Usage

usage: tagore.py [-h] [--version] -i <input.bed> [-p [output file prefix]] [-v] [-f]

tagore: a utility for illustrating human chromosomes

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"]
  -v, --verbose                                           Display verbose output
  -f, --force                                             Overwrite output files if they exist already

The 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 the scripts/ folder.

A more complete example of a full chromosome painting using an RFMix output can be seen by running:

./scripts/rfmix2tagore.py --chr1 example_ideogram/1KGP-MXL104_chr1.bed \
	--chr2 example_ideogram/1KGP-MXL104_chr2.bed \
	--out example_ideogram/1KGP-MXL104_tagore.bed

tagore -input example_ideogram/1KGP-MXL104_tagore.bed \
	--prefix example_ideogram/1KGP-MXL104 \
  --build hg37
  --verbose

Input 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	1

Each column is explained below:

  1. chr - The chromosome on which a feature has to be drawn
  2. start - Start position (in bp) for feature
  3. stop - Stop position (in bp) for feature
  4. feature - The shape of the feature to be drawn
    • 0 will draw a rectangle
    • 1 will draw a circle
    • 2 will draw a triangle pointing to the genomic location
    • 3 will draw a line at that genomic location
  5. size - The horizontal size of the feature. Should range between 0 and 1.
  6. color - Specify the color of the genomic feature with a hex value (#FF0000 for red, etc.)
  7. 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 twice

Etymology

Tagore (/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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for tagore, version 1.0.1
Filename, size File type Python version Upload date Hashes
Filename, size tagore-1.0.1-py3-none-any.whl (24.5 kB) File type Wheel Python version py3 Upload date Hashes View hashes
Filename, size tagore-1.0.1.tar.gz (13.4 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page