/usr/bin/render_msa is in libbio-graphics-perl 2.40-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 | #!/usr/bin/perl
use strict;
use Bio::Graphics;
use Bio::AlignIO;
use Bio::SeqFeature::Generic;
use Bio::Tools::GuessSeqFormat;
use Getopt::Long;
my ($inputfile,$debug);
GetOptions(
'i|input|inputfile:s' => \$inputfile,
'debug' => \$debug,
);
my $guessed_format = new Bio::Tools::GuessSeqFormat
(-file=>"$inputfile"
)->guess;
my $aio = Bio::AlignIO->new(-file => $inputfile,
-format => $guessed_format) or die "parse failed";
my $aln = $aio->next_aln() or die "no alignment";
my $panel = Bio::Graphics::Panel->new(
-image_class => 'SVG',
-length => $aln->length,
-width => 800,
-pad_left => 150,
-pad_right => 10,
);
my $full_length = Bio::SeqFeature::Generic->new(
-start => 1,
-end => $aln->length,
-display_name => 'fasta alignment',
);
$panel->add_track($full_length,
-glyph => 'arrow',
-tick => 2,
-fgcolor => 'black',
-double => 1,
-label => 1,
);
my $track = $panel->add_track(
-glyph => 'segments',
-label => 1,
-connector => 'dashed',
-bgcolor => 'green',
-label_position => 'alignment_left',
-font2color => 'red'
);
for my $seqobj ($aln->each_seq) {
my $seq = $seqobj->seq;
my @seqs;
# get alignment positions for seqs
my $feature = Bio::SeqFeature::Generic->new(
-display_name => $seqobj->get_nse,
);
while ($seq =~ m{([^-]+)}g) {
# zero-based coords, must adjust accordingly
$feature->add_sub_SeqFeature(
Bio::SeqFeature::Generic->new(-start => pos($seq)-length($1)+1,
-end => pos($seq),
-sequence => $1), 'EXPAND');
}
$track->add_feature($feature);
}
print $panel->svg;
|