NAME

Bio::Grid::Run::SGE::Iterator::AllvsAll - Runs all elements of one index against each other

SYNOPSIS

            

              
              
use Bio::Grid::Run::SGE::Iterator::AllvsAll;
use Bio::Grid::Run::SGE::Index;
# the dummy index contains the letters a..c as elements
my $index = Bio::Grid::Run::SGE::Index->new( format => 'Dummy', idx_file => undef, idx => [ 'a'..'c'] )->create;
my $it = Bio::Grid::Run::SGE::Iterator::AllvsAll->new( indices => [$index] );
# run through all combinations
my ($from, $to) = (0, $it->num_comb - 1);
$it->range( [ $from, $to]  );
my @result;
my $i = $from;
while ( my $comb = $it->next_comb ) {
  print "job " . $i++ . " -> " . join(" ",  $comb->[0], $comb->[1] ) . "\n";
}
            
          

DESCRIPTION

Runs all elements of the index against each other. Takes exactly one index. Results in N * N jobs with N as number of elements in the index.

The difference to Bio::Grid::Run::SGE::Iterator::AllvsAllNoRep is that it does NOT assume symmetry. Thus, runing element x vs y is different from running y vs x.

ITERATION SCHEME

An index with 3 elements (a..c) combines to:

            

              
              
job 1 -> a a
job 2 -> a c
job 3 -> a b
job 4 -> b a
job 5 -> b b
job 6 -> b c
job 7 -> c a
job 8 -> c b
job 9 -> c c
            
          

CONFIGURATION

            

              
              
---
...
mode: AllvsAll
...
            
          

COMPLETE EXAMPLE

CONFIG FILE

            

              
              
---
input:
  - format: List
    elements: [ "a", "b", "c" ]
job_name: AllvsAll_test
mode: AllvsAll
            
          

CLUSTER SCRIPT

            

              
              
#!/usr/bin/env perl
use warnings;
use strict;
use 5.010;
use Bio::Grid::Run::SGE;
use File::Spec::Functions qw(catfile);
use Bio::Grid::Run::SGE::Util qw(result_files);
run_job(
  task => \&do_worker_stuff
);
sub do_worker_stuff {
  my ( $c, $result_prefix, $elems_a, $elems_b ) = @_;
  # write results to result prefix (== result file)
  open my $fh, '>', $result_prefix or die "Can't open filehandle: $!";
  # because we have list indices, $elems_a and $elems_b are (paired) array references
  # other indices might give file names instead, so check the documentation
  my $num_elems = @$elems_a;
  for ( my $i = 0; $i < @$elems_a; $i++ ) {
    say $fh join( " ", $elems_a->[$i], $elems_b->[$i] );
  }
  $fh->close;
  # return 1 on success
  return 1;
}
1;
            
          

SEE ALSO

Bio::Grid::Run::SGE::Role::Iterable, Bio::Grid::Run::SGE::Iterator

AUTHOR

jw bargsten, <jwb at cpan dot org>