# last-dotplot

This script makes a dotplot, a.k.a. Oxford Grid, of pair-wise sequence alignments in MAF or LAST tabular format. It requires the Python Imaging Library to be installed. It can be used like this:

    last-dotplot my-alignments my-plot.png

The output can be in any format supported by the Imaging Library:

    last-dotplot alns alns.gif

To get a nicer font, try something like:

    last-dotplot -f /usr/share/fonts/truetype/freefont/FreeSans.ttf alns alns.png

If the fonts are located somewhere different on your computer, change this as appropriate.

## Choosing sequences

If there are too many sequences, the dotplot will be very cluttered, or the script might give up with an error message. You can exclude sequences with names like "chrUn_random522" like this:

    last-dotplot -1 'chr[!U]*' -2 'chr[!U]*' alns alns.png

Option "-1" selects sequences from the 1st genome, and "-2" selects sequences from the 2nd genome. 'chr[!U]*' is a pattern that specifies names starting with "chr", followed by any character except U, followed by anything.

Pattern | Meaning
`*` | zero or more of any character
`?` | any single character
`[abc]` | any character in abc
`[!abc]` | any character not in abc

If a sequence name has a dot (e.g. "hg19.chr7"), the pattern is compared to both the whole name and the part after the dot.

You can specify more than one pattern, e.g. this gets sequences with names starting in "chr" followed by one or two characters:

    last-dotplot -1 'chr?' -1 'chr??' alns alns.png

## Options

> `-h, --help` | Show a help message, with default option values, and exit.
> `-1 PATTERN, --seq1=PATTERN` | Which sequences to show from the 1st genome.
> `-2 PATTERN, --seq2=PATTERN` | Which sequences to show from the 2nd genome.
> `-x WIDTH, --width=WIDTH` | Maximum width in pixels.
> `-y HEIGHT, --height=HEIGHT` | Maximum height in pixels.
> `-f FILE, --fontfile=FILE` | TrueType or OpenType font file.
> `-s SIZE, --fontsize=SIZE` | TrueType or OpenType font size.
> `-c COLOR, --forwardcolor=COLOR` | Color for forward alignments.
> `-r COLOR, --reversecolor=COLOR` | Color for reverse alignments.

### Unsequenced gap options

Note: these "gaps" are not alignment gaps (indels): they are regions of unknown sequence.

> `--gap1=FILE` | Read unsequenced gaps in the 1st genome from an agp or gap file.
> `--gap2=FILE` | Read unsequenced gaps in the 2nd genome from an agp or gap file.
> `--bridged-color=COLOR` | Color for bridged gaps.
> `--unbridged-color=COLOR` | Color for unbridged gaps.

An unsequenced gap will be shown only if it covers at least one whole pixel.