Joachim Bargsten

NAME

SYNOPSIS

  #wenn export, dann hier im qw()
  my $idx = Bio::Grid::Run::SGE::Index::General->new(
    'idx_file' => $idx_file,
    'sep'      => '^>'
    'sep_pos' => '^',
    'sep_remove' => 1,
    'ignore_first_sep' => 1,

  );

DESCRIPTION

sep_remove

remove the separators between the data records. For sep remove sth. like

  <FILE_START>
  <entry1>
  <sep>
  <entry2>
  <sep>
  ...
  <sep>
  <entryN>
  <FILE_END>

is expected, so no separator at begin or end of file, otherwise it will break! If you have a separator before the first data record, you can use the ignore_first_sep option to skip over it.

sep_pos

Can be '^' or '$'. '^' corresponds to a file layout

  <FILE_START>
  <sep> <--- NOTE: the first sep
  <entry1>
  <sep>
  <entry2>
  <sep>
  ...
  <sep>
  <entryN> <--- NOTE: no last sep
  <FILE_END>

'$' corresponds to a file layout:

  <FILE_START>
  <entry1><--- NOTE: no first sep
  <sep>
  <entry2>
  <sep>
  ...
  <sep>
  <entryN>
  <sep> <--- NOTE: the last sep
  <FILE_END>

OPTIONS

SUBROUTINES =head1 METHODS

SEE ALSO

AUTHOR

jw bargsten, <jwb at cpan dot org>