exonviz 0.2.5

Visualise exons and their reading frames

Exonviz

Visualise exons

Installation

Exonviz only requires Python, and can be installed using PIP:

pip install exonviz

Usage

Pass either a transcript (with version!), or a valid HGVS description to exonviz to generate a figure.

Options

Since each gene is different, you will probably want to play around with the options to get the perfect figure for your favorite gene.

usage: exonviz [-h] [--width WIDTH] [--height HEIGHT] [--scale SCALE]
               [--noncoding] [--gap GAP] [--color COLOR] [--exonnumber]
               [--firstexon FIRSTEXON] [--lastexon LASTEXON]
               [--variantcolors VARIANTCOLORS [VARIANTCOLORS ...]]
               [--dump-exons DUMP_EXONS] [--dump-variants DUMP_VARIANTS]
               (--transcript TRANSCRIPT | --exon-tsv EXON_TSV)
               [--variant-tsv VARIANT_TSV]

Visualise exons and mutations

options:
  -h, --help            show this help message and exit
  --width WIDTH         Maximum width of the figure (default: 9999999)
  --height HEIGHT       Exon height (default: 20)
  --scale SCALE         Scale (pixels per bp) (default: 1.0)
  --noncoding           Show non coding regions (default: False)
  --gap GAP             Gap between the exons (default: 5)
  --color COLOR         Color for the exons (e.g. 'purple') (default: #4C72B7)
  --exonnumber          Show exon number (default: False)
  --firstexon FIRSTEXON
                        The first exon to draw (default: 1)
  --lastexon LASTEXON   The last exon to draw (default: 9999)
  --variantcolors VARIANTCOLORS [VARIANTCOLORS ...]
                        List of variant colors to cycle through (default:
                        ['#BA1C30', '#DB6917', '#EBCE2B', '#702C8C',
                        '#C0BD7F'])
  --dump-exons DUMP_EXONS
                        Write exons to the specified file (default: None)
  --dump-variants DUMP_VARIANTS
                        Write variants to the specified file (default: None)
  --transcript TRANSCRIPT
                        Transcript (with version) to visualise (default: None)
  --exon-tsv EXON_TSV   TSV file containing exons (default: None)
  --variant-tsv VARIANT_TSV
                        TSV file containing variants (default: None)

Examples

SDHD

Using the default settings, which does not include non-coding regions of the transcript:

exonviz --transcript SDHD > SDHD.svg

DMD

For DMD, we explicitly specify the transcript we are interested in. We also set a maximum width for the figure, since DMD has many exons:

exonviz --transcript "NM_004006.3" --width 1024 --color purple --exonnumber > DMD.svg

ATXN1

Include the non coding exons, since most exons of ATXN1 are non coding. We limit the maximum width and increase the height of the picture. For clarity, we also increase the distance between the displayed exons:

exonviz --transcript ENST00000436367.6 --noncoding --width 4000 --height 150 --gap 50 > ATXN1.svg

PLP1

You can also input a valid HGVS description on the transcript of interest. The variant will be ignored. Include the non coding regions and increase the height and distance between the exons:

exonviz --transcript "NM_000533.5:c.100G>T" --height 100 --gap 50 --scale 6.5 > PLP1.svg

NF1

Set the maximum width of the figure to the approximate size of the largest exon:

exonviz --transcript "ENST00000358273.9" --noncoding --width 3600 --height 75 --gap 20 > NF1-202.svg