4 This script makes a dotplot, a.k.a. Oxford Grid, of pair-wise sequence
5 alignments in MAF or LAST tabular format. It requires the Python
6 Imaging Library to be installed. It can be used like this::
8 last-dotplot my-alignments my-plot.png
10 The output can be in any format supported by the Imaging Library::
12 last-dotplot alns alns.gif
14 To get a nicer font, try something like::
16 last-dotplot -f /usr/share/fonts/truetype/freefont/FreeSans.ttf alns alns.png
18 If the fonts are located somewhere different on your computer, change
24 If there are too many sequences, the dotplot will be very cluttered,
25 or the script might give up with an error message. You can exclude
26 sequences with names like "chrUn_random522" like this::
28 last-dotplot -1 'chr[!U]*' -2 'chr[!U]*' alns alns.png
30 Option "-1" selects sequences from the 1st genome, and "-2" selects
31 sequences from the 2nd genome. 'chr[!U]*' is a *pattern* that
32 specifies names starting with "chr", followed by any character except
33 U, followed by anything.
35 ========== =============================
37 ---------- -----------------------------
38 ``*`` zero or more of any character
39 ``?`` any single character
40 ``[abc]`` any character in abc
41 ``[!abc]`` any character not in abc
42 ========== =============================
44 If a sequence name has a dot (e.g. "hg19.chr7"), the pattern is
45 compared to both the whole name and the part after the dot.
47 You can specify more than one pattern, e.g. this gets sequences with
48 names starting in "chr" followed by one or two characters::
50 last-dotplot -1 'chr?' -1 'chr??' alns alns.png
52 You can also specify a sequence range; for example this gets the first
55 last-dotplot -1 chr9:0-1000 alns alns.png
61 Show a help message, with default option values, and exit.
62 -1 PATTERN, --seq1=PATTERN
63 Which sequences to show from the 1st genome.
64 -2 PATTERN, --seq2=PATTERN
65 Which sequences to show from the 2nd genome.
66 -x WIDTH, --width=WIDTH
67 Maximum width in pixels.
68 -y HEIGHT, --height=HEIGHT
69 Maximum height in pixels.
70 -f FILE, --fontfile=FILE
71 TrueType or OpenType font file.
72 -s SIZE, --fontsize=SIZE
73 TrueType or OpenType font size.
74 -c COLOR, --forwardcolor=COLOR
75 Color for forward alignments.
76 -r COLOR, --reversecolor=COLOR
77 Color for reverse alignments.
79 Trim unaligned sequence flanks from the 1st genome.
81 Trim unaligned sequence flanks from the 2nd genome.
84 <https://genome.ucsc.edu/FAQ/FAQformat.html#format1>`_
85 annotations for the 1st genome. They are drawn as rectangles,
86 with coordinates given by the first three BED fields. The color
87 is specified by the RGB field if present, else pale red if the
88 strand is "+", pale blue if "-", or pale purple.
90 Read BED-format annotations for the 2nd genome.
92 Unsequenced gap options
93 ~~~~~~~~~~~~~~~~~~~~~~~
95 Note: these "gaps" are *not* alignment gaps (indels): they are regions
99 Read unsequenced gaps in the 1st genome from an agp or gap file.
101 Read unsequenced gaps in the 2nd genome from an agp or gap file.
102 --bridged-color=COLOR
103 Color for bridged gaps.
104 --unbridged-color=COLOR
105 Color for unbridged gaps.
107 An unsequenced gap will be shown only if it covers at least one whole