Usage

Installation

ExonViz can be installed using pip:

pip install exonviz

Default usage

exonviz --transcript DMD > DMD.svg

Command line

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: 0)
  --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)