Verticall mask

The verticall mask command is part of the alignment tree workflow (see that page for example commands). It takes the TSV file made by verticall pairwise and a whole-genome pseudo-alignment, and it produces a version of the alignment with horizontal regions masked out.

Full help output

usage: verticall mask -i IN_TSV -a IN_ALIGNMENT -o OUT_ALIGNMENT [--image IMAGE]
                      [--vertical_colour VERTICAL_COLOUR] [--horizontal_colour HORIZONTAL_COLOUR]
                      [--unaligned_colour UNALIGNED_COLOUR] [--reference REFERENCE]
                      [--multi {first,exclude,low,high}] [--h_char H_CHAR] [--u_char U_CHAR]
                      [--exclude_invariant] [--exclude_reference] [-h] [--version]

mask horizontal regions from a whole-genome pseudo-alignment

Required arguments:
  -i IN_TSV, --in_tsv IN_TSV       Filename of TSV created by vertical pairwise
  -a IN_ALIGNMENT, --in_alignment IN_ALIGNMENT
                                   Filename of whole-genome pseudo-alignment to be masked
  -o OUT_ALIGNMENT, --out_alignment OUT_ALIGNMENT
                                   Filename of masked whole-genome pseudo-alignment

Illustration:
  --image IMAGE                    Filename of SVG illustration of masked regions (optional)
  --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)

Settings:
  --reference REFERENCE            Sample name for the reference genome (default: determine
                                   automatically if possible from the TSV file)
  --multi {first,exclude,low,high}
                                   Behaviour when there are multiple results for a sample pair
                                   (default: first)
  --h_char H_CHAR                  Character used to mask horizontal regions (default: N, use None to
                                   leave horizontal regions unmasked)
  --u_char U_CHAR                  Character used to mask unaligned regions (default: -, use None to
                                   leave unaligned regions unmasked)
  --exclude_invariant              Only include variant sites in the output alignment (default: include
                                   both variant and invariant sites in the output alignment)
  --exclude_reference              Do not include the reference sequence in the output alignment
                                   (default: include the reference sequence in the output alignment)

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