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|
#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fasta_reader;
print STDERR "\n\n\tNOTE - longest transcript isn't always the best transcript!... consider filtering based on relative expression support ... \n\n";
my $usage = "usage: $0 Trinity.fasta\n\n";
my $trin_fasta = $ARGV[0] or die $usage;
main: {
my %gene_to_longest_transcript;
my $fasta_reader = new Fasta_reader($trin_fasta);
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my $header = $seq_obj->get_header();
my $gene_id;
if ($acc =~ /^(.*comp\d+_c\d+)_seq/) {
$gene_id = $1;
}
elsif ($acc =~ /^(.*c\d+_g\d+)_i/) {
$gene_id = $1;
}
unless ($gene_id) {
die "Error, cannot parse gene identifier from acc: $acc";
}
my $sequence = $seq_obj->get_sequence();
if ( (! exists $gene_to_longest_transcript{$gene_id})
||
$gene_to_longest_transcript{$gene_id}->{length} < length($sequence)) {
$gene_to_longest_transcript{$gene_id} = { length => length($sequence),
acc => $acc,
sequence => $sequence,
header => $header,
};
}
}
foreach my $longest_seq ( reverse sort {$a->{length}<=>$b->{length}} values %gene_to_longest_transcript) {
print ">" . $longest_seq->{header} . "\n" . $longest_seq->{sequence} . "\n";
}
print STDERR "\n\nok. Done.\n\n";
exit(0);
}
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