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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.
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