dirwatch-translate.pl

#!/usr/bin/perl
use Modern::Perl;
use POE qw(Component::DirWatch::Object::NewFile);
use Bio::SeqIO;
use Bio::Seq;
use File::Temp;
use File::Copy qw(move);
use Gtk2::Notify -init, "Translator";

my $watcher = POE::Component::DirWatch::Object::NewFile->new(
    directory => '/home/brunov/translate',
    filter    => sub { $_[0] =~ /\.fasta/ && -f $_[1] },    # Only fasta
    callback  => sub {
        eval { translate(@_) };
    },
    interval => 1,                                          # Watch interval
);

# Different ways of passing a message to the user.
my %notify_with = (
    gtk2    => sub { Gtk2::Notify->new( 'Attention', shift )->show },
    stdout  => sub { say shift },
    stderr  => sub { warn shift, "\n" },
    nothing => sub { return },
);

sub translate {

    # Translate the input file from dna to protein, replacing the
    # original file. Sequences that are already protein remain
    # untouched.

    my ( $filename, $fullpath ) = @_;

    # Input sequence stream.
    my $seqI = Bio::SeqIO->new( -file => $fullpath );

    # Output sequence stream.
    my $tempfile = File::Temp->new( SUFFIX => '.fasta' )->filename;
    my $seqO = Bio::SeqIO->new( -file => ">$tempfile", format => 'fasta' );

    # Translate dna sequences and write to temp file.
    my $outcome = 0;
    while ( my $seq = $seqI->next_seq ) {
        if ( $seq->alphabet eq 'dna' ) {
            $seq     = $seq->translate;
            $outcome = 1;
        }
        $seqO->write_seq($seq);
    }

    $_->close for ( $seqI, $seqO );

    # Replace the original file with the temporary one with the
    # translated sequences.
    # $outcome will be true only if seq is dna and move succeded.
    $outcome *= move( $tempfile, $fullpath );

    notify( $outcome, $filename, qw(gtk2 stderr) );
}

sub notify {
    my ( $success, $file, @mediums ) = @_;

    if ($success) {
        $notify_with{$_}->("Translated $file") for @mediums;
    } else {
        $notify_with{$_}->("$file not translated") for @mediums;
    }

    return 1;
}

$poe_kernel->run();