fix_tRNA_annotation.pl

#!/usr/bin/perl

use lib $ENV{SCRIPTS};
use ENV;
use strict;
use Getopt::Std;
use Bio::SeqFeature::Generic;
use DBI;

my $args = {};
&getopts('i:d:u:p:', $args);
my $DEBUG = 0;
my $input_file=$args->{i};
my $db = $args->{d};
my $pwd = $args->{p};
my $user = $args->{u} ? $args->{u} : $ENV{USER};
my $host = $ENV{DBSERVER} ? $ENV{DBSERVER} : 'localhost';

my $dbh = DBI->connect("dbi:mysql:host=$host;db=$db", $user, $pwd);

open (my $IN, $input_file) or die "Can't open $input_file: $!\n";

my %AA;
while (my $line = <$IN>) {
    chomp $line;
    my ($seq_acc,
	$index,
	$end5,
	$end3,
	$aa,
	$acodon,
	$intron_end5,
	$intron_end3,
	$score) = split /\s+/, $line;
    if ($index !~ /\d+/) { next }
    my @accs = split/\|/, $seq_acc;
    my $sid;
    my $sacc;
    foreach my $ax(@accs) {
	$sid = get_seq_id_by_seq_accession($dbh, $ax);
	$sacc = $ax;
	if ($sid) { last }
    }
    if (!$sid) { die " Couldn't get a sequence_id from the accession '$seq_acc'.\n" }

    my ($start, $end, $strand) = $end5 < $end3 ? ($end5, $end3, 1) : ($end3, $end5, -1);
    $AA{$aa}++;
    my $id = $sacc . "-tRNA-$index";
    my $name = "tRNA-$aa-$AA{$aa}";

    my $feature_q = "select feature_id from seq_feat_mappings where seq_id=$sid and (feat_min=$start or feat_max=$end) and strand='$strand'";
    my ($fid) = $dbh->selectrow_array($feature_q);
    if (! $fid) { print STDERR "Couldn't find feature_id for \n$line\n$feature_q\n"; next; }
    else { print STDERR "FOUND feature_id $fid for\n$line\n" if ($DEBUG);}

    my $annObj = Bio::Annotation::Collection->new();
    $annObj->add_Annotation("product",
			    Bio::Annotation::SimpleValue->new(-value=>$name));
    $annObj->add_Annotation("anticodon",
			    Bio::Annotation::SimpleValue->new(-value=>$acodon));

    delete_feature_annotations($dbh, $fid);
    load_feature_annotations($dbh, $fid, $annObj, "tRNAscan-SE", 3);
}