genome2plot.py

The script genome2plot.py aims to plot a genome and displays the structural variations provided. The script needs two bed files as input:

1. A 4-column bed file (chr, start, end, type) with the coordinates of the corresponding structural variations. Allowed type values: INS (insertions), DEL (deletions), DUP (duplications), INV (inversions), TRA (transversions). E.g. structuralvariations.bed.
2. A 3-column bed file (chr, 1, end) providing chromosome lengths. E.g. genome.bed.

Example:

genome2plot.py structuralvariations.bed genome.bed

The output should be something like this:

For a proper visualization, only chromosomes larger than the 5% of the largest chromosome length are displayed (thus, small scaffolds not displayed). Structural variations are represented by different colours. Colour dictionary:

{
'DUP': 'Red',
'DEL': 'Lime',
'INS': 'DarkOrange',
'INV': 'SteelBlue',
'TRA': 'Gainsboro'
}