Verticall summary

The verticall summary command is an optional step to summary the painting of one assembly relative to all other assemblies. It takes the TSV file made by verticall pairwise and produces either:

• a tab-delimited table (printed to stdout) which shows the number of vertical, horizontal and unaligned paintings.
• an interactive plot visualising the table data

Example usage

To produce a table:

verticall summary -i verticall.tsv -a assemblies/abc.fasta

To produce an interactive plot:

verticall summary -i verticall.tsv -a assemblies/abc.fasta --plot

Example plot

Here's an example plot showing the summary for a Klebsiella variicola assembly in a collection of 210 assemblies spanning the Klebsiella pneumoniae species complex:

This was a completed assembly, which makes for a cleaner summary plot. Contigs are separated by solid vertical lines (most of the plot is the big chromosomal contig). The data is shown as a stacked area plot, where blue is vertical, red is horizontal and grey is unaligned. These three values total to 209 (the number of other assemblies) at each position. For most of the assembly, this genome is vertical compared to the other assemblies, indicated by the blue. However, two large pieces of the chromosome are mostly horizontal (this was a case of cross-species recombination). And a few pieces of the assembly (especially in the plasmid contigs) are mostly unaligned, indicating accessory genome.

Full help output

usage: verticall summary -i IN_FILE -a ASSEMBLY [--all] [--plot] [--vertical_colour VERTICAL_COLOUR]
                         [--horizontal_colour HORIZONTAL_COLOUR] [--unaligned_colour UNALIGNED_COLOUR]
                         [-h] [--version]

summarise regions for one assembly

Required arguments:
  -i IN_FILE, --in_file IN_FILE    Filename of TSV created by vertical pairwise
  -a ASSEMBLY, --assembly ASSEMBLY
                                   Filename of assembly to be summarised

Settings:
  --all                            Output one line for all assembly positions (default: omit redundant
                                   adjacent lines)
  --plot                           Instead of outputting a table, display an interactive plot (default:
                                   do not display a plot)

Colours:
  --vertical_colour VERTICAL_COLOUR
                                   Hex colour for vertical inheritance (default: #4859a0)
  --horizontal_colour HORIZONTAL_COLOUR
                                   Hex colour for horizontal inheritance (default: #c47e7e)
  --unaligned_colour UNALIGNED_COLOUR
                                   Hex colour for unaligned inheritance (default: #c9c9c9)

Other:
  -h, --help                       Show this help message and exit
  --version                        Show program's version number and exit