NAME

  Bio::Grid::Run::SGE::Iterator::Consecutive - iterate consecutively through an index

SYNOPSIS

    use Bio::Grid::Run::SGE::Iterator::Consecutive;
    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 $it = Bio::Grid::Run::SGE::Iterator::Consecutive->new( indices => [$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++ . " -> " . $comb->[0] . "\n";
    }

DESCRIPTION

This is the simplest iterator, it runs through a range of elements in an index. It takes exactly one index. Results in N opeations with N as number of elements in the index.

ITERATION SCHEME

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

  job 1 -> a
  job 2 -> b
  job 3 -> c

CONFIGURATION

  ---
  ...
  mode: Consecutive
  ...

COMPLETE EXAMPLE

CONFIG FILE

    ---
    input:
      - format: List
        elements: [ "a", "b", "c" ]
    job_name: Consecutive_test
    mode: Consecutive

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 ) = @_;

      # write results to result prefix (== result file)
      open my $fh, '>', $result_prefix or die "Can't open filehandle: $!";

      # because we have a list index, $elems_a is an array reference
      # 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 $elems_a->[$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>