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|
#!/usr/bin/env perl
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use strict;
use warnings;
use Getopt::Std;
use Fasta_reader;
use Longest_orf;
use List::Util qw (min max);
use Bio::Graphics;
use Bio::SeqFeature::Generic;
my $usage = "\n\nusage: $0 transcripts.fasta\n\n";
my $transcripts_fasta_file = $ARGV[0] or die $usage;
my $min_prot_len = 50;
main: {
my $fasta_reader = new Fasta_reader($transcripts_fasta_file);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my $sequence = $seq_obj->get_sequence();
my $seq_length = length($sequence);
my $panel = Bio::Graphics::Panel->new(
-length => $seq_length,
-width => 800,
-pad_left => 10,
-pad_right => 10,
);
my $full_length = Bio::SeqFeature::Generic->new(
-start => 1,
-end => $seq_length,
-strand => 1,
-display_name => $acc,
);
## add ticker
$panel->add_track($full_length,
-glyph => 'arrow',
-tick => 2,
-fgcolor => 'black',
-double => 1,
);
## add feature
$panel->add_track($full_length,
-glyph => 'transcript2',
-bgcolor => 'black',
-label => 1,
);
my $longest_orf_finder = new Longest_orf();
$longest_orf_finder->allow_5prime_partials();
$longest_orf_finder->allow_3prime_partials();
my @orf_structs = $longest_orf_finder->capture_all_ORFs($sequence);
@orf_structs = reverse sort {$a->{length}<=>$b->{length}} @orf_structs;
my $top_track = $panel->add_track(-glyph => 'transcript2',
-label => 1,
-strand_arrow => 1,
-bgcolor => 'blue',
);
my $bottom_track = $panel->add_track(-glyph => 'transcript2',
-label => 1,
-strand_arrow => 1,
-bgcolor => 'red',
);
my $pep_file = "$acc.orfs.pep";
my $cds_file = "$acc.orfs.cds";
open (my $pep_ofh, ">$pep_file") or die "Error, cannot write to $pep_file";
open (my $cds_ofh, ">$cds_file") or die "Error, cannot write to $cds_file";
foreach my $orf (@orf_structs) {
my $start = $orf->{start};
my $stop = $orf->{stop};
if ($stop <= 0) { $stop += 3; } # edge issue
my $length = int($orf->{length}/3);
if ($length < $min_prot_len) { next; }
my $orient = $orf->{orient};
my $protein = $orf->{protein};
my $cds = $orf->{sequence};
my $frame = $start % 3;
if ($frame == 0) {
$frame = 3;
}
my $orf_name = "$acc.$start-$stop.F$frame";
print $pep_ofh ">$orf_name\n$protein\n";
print $cds_ofh ">$orf_name\n$cds\n";
if ($orient eq '+') {
my $feature = Bio::SeqFeature::Generic->new(
-start => $start,
-end => $stop,
-display_name => "orf: $start-$stop (F:$frame)",
-strand => 1,
);
$top_track->add_feature($feature);
}
else {
# minus strand
$frame = -1 * $frame;
my $feature = Bio::SeqFeature::Generic->new(
-start => $start,
-end => $stop,
-display_name => "orf: $start-$stop (F:$frame)",
-strand => -1,
);
$bottom_track->add_feature($feature);
}
}
close $pep_ofh;
close $cds_ofh;
my $img_filename = "$acc.orf.png";
print STDERR "-writing: $img_filename\n";
open (my $ofh, ">$img_filename") or die "Error, cannot write to file $img_filename";
binmode($ofh);
print $ofh $panel->png();
close $ofh;
}
exit(0);
}
|
