#! /usr/bin/perl
use strict;
use warnings;

my @sorted =
  map { $_->[0] }
    sort {
        $a->[1] <=> $b->[1]     ||
        $a->[2] <=> $b->[2]     ||
        $a->[3] <=> $b->[3]
    }
      map { [ $_, map { defined $_ ? $_ : 0 } (split /\s+/, $_)[1,5,7] ] } <DATA>;

use Data::Dumper;
print Dumper \@sorted;


__DATA__
locus 1 transcript 3/12 confidence 11.000 length 238
locus 2 transcript 3/12 confidence 12.000 length 238
locus 5 transcript 3/12 confidence 15.000 length 238
locus 3 transcript 3/12 confidence 13.000 length 238
locus 6 transcript 3/12 confidence 16.000 length 238
locus 4 transcript 3/12 confidence 14.000 length
locus 1 transcript 3/12 confidence 11.000 length 138