NAME

Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format).

SYNOPSIS

    # Complete code for making an index for several
    # EMBL files
    use Bio::Index::EMBL;

    my $Index_File_Name = shift;
    my $inx = Bio::Index::EMBL->new($Index_File_Name, 'WRITE');
    $inx->make_index(@ARGV);

    # Print out several sequences present in the index
    # in gcg format
    use Bio::Index::EMBL;

    my $Index_File_Name = shift;
    my $inx = Bio::Index::EMBL->new($Index_File_Name);

    foreach my $id (@ARGV) {
        my $seq = $inx->fetch($id); # Returns Bio::Seq object
        print $seq->layout('GCG');
    }

    # alternatively

    my $seq1 = $inx->get_Seq_by_id($id);
    my $seq2 = $inx->get_Seq_by_acc($acc);   

DESCRIPTION

Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing EMBL files, and retrieving the sequence from them. Heavily snaffled from James Gilbert's Fasta system.

FEED_BACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
  vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
  http://bio.perl.org/MailList.html             - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Ewan Birney

Email - birney@sanger.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_initialize

  Title   : _initialize
  Usage   : $index->_initialize
  Function: Calls $index->SUPER::_initialize(), and then adds
            the default id parser for EMBL files.
  Example : 
  Returns : 
  Args    : 

_index_file

  Title   : _index_file
  Usage   : $index->_index_file( $file_name, $i )
  Function: Specialist function to index EMBL format files.
            Is provided with a filename and an integer
            by make_index in its SUPER class.
  Example : 
  Returns : 
  Args    : 

fetch

  Title   : fetch
  Usage   : $index->fetch( $id )
  Function: Returns a Bio::Seq object from the index
  Example : $seq = $index->fetch( 'dJ67B12' )
  Returns : Bio::Seq object
  Args    : ID

get_Seq_by_id

 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id()
 Function: retrieves a sequence object, identically to
           ->fetch, but here behaving as a Bio::DB::BioSeqI
 Returns : new Bio::Seq object
 Args    : string represents the id

get_Seq_by_acc

 Title   : get_Seq_by_acc
 Usage   : $seq = $db->get_Seq_by_acc()
 Function: retrieves a sequence object, identically to
           ->fetch, but here behaving as a Bio::DB::BioSeqI
 Returns : new Bio::Seq object
 Args    : string represents the accession number