/ 
BioPerl-1.7.8
River stage two • 61 direct dependents • 66 total dependents
/ Bio::Index::GenBank

NAME

Bio::Index::GenBank - Interface for indexing one or more GenBank files (i.e. flat file GenBank format).

SYNOPSIS

    # Complete code for making an index for one or more GenBank files
    use strict;
    use Bio::Index::GenBank;

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

    # Print out sequences present in the index in gcg format
    use Bio::Index::GenBank;
    use Bio::SeqIO;
    use strict;

    my $Index_File_Name = shift;
    my $inx = Bio::Index::GenBank->new(-filename => $Index_File_Name);
    my $seqio = Bio::SeqIO->new(-format => 'gcg');
    foreach my $id (@ARGV) {
        my $seq = $inx->fetch($id); # Returns Bio::Seq object
        $seqio->write_seq($seq);
    }

    # alternatively
    my ($locus, $acc);
    my $seq1 = $inx->get_Seq_by_id($locus);
    my $seq2 = $inx->get_Seq_by_acc($acc);

DESCRIPTION

By default the index that is created uses the LOCUS, ACCESSION, and VERSION identifiers as keys. Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic functionality for indexing GenBank files, and retrieving the sequence from them. For best results 'use strict'.

You can also set or customize the unique key used to retrieve by writing your own function and calling the id_parser() method. For example:

$inx->id_parser(\&get_id);
# make the index
$inx->make_index($file_name);

# here is where the retrieval key is specified
sub get_id {
   my $line = shift;
   $line =~ /clone="(\S )"/;
   $1;
}

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.

[email protected]                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

Email - [email protected]

APPENDIX

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

_index_file

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

id_parser

Title   : id_parser
Usage   : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
          parse the ID for record from a string.
          Returns \&default_id_parser (see below) if not
          set. An entry will be added to
          the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : reference to CODE if called without arguments
Args    : CODE

default_id_parser

Title   : default_id_parser
Usage   : $id = default_id_parser($line)
Function: The default parser for GenBank.pm
Returns : Array of specified ids
Args    : a line string

_file_format

Title   : _file_format
Usage   : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns : 
Args    :