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Bio::Index::Swissprot.3pm

NAME

Bio::Index::Swissprot - Interface for indexing one or more Swissprot files.

SYNOPSIS

   # Make an index for one or more Swissprot files:
 
     use Bio::Index::Swissprot;
     use strict;
 
     my $index_file_name = shift;
     my $inx = Bio::Index::Swissprot->new(
         -filename => $index_file_name,
         -write_flag => 1);
     $inx->make_index(@ARGV);
 
   # Print out several sequences present in the index in Genbank
   # format:
 
     use Bio::Index::Swissprot;
     use Bio::SeqIO;
     use strict;
 
     my $out = Bio::SeqIO->new( -format => 'genbank',
                                -fh => \*STDOUT );
     my $index_file_name = shift;
     my $inx = Bio::Index::Swissprot->new(-filename => $index_file_name);
 
     foreach my $id (@ARGV) {
         my $seq = $inx->fetch($id); # Returns a Bio::Seq object
         $out->write_seq($seq);
     }
 
     # alternatively
     my ($id, $acc);
     my $seq1 = $inx->get_Seq_by_id($id);
     my $seq2 = $inx->get_Seq_by_acc($acc);
 
 

DESCRIPTION

By default the index that is created uses the AC and ID identifiers as keys. This module inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic functionality for indexing Swissprot files and retrieving Sequence objects 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
    $inx->make_index($index_file_name);
 
    # here is where the retrieval key is specified
    sub get_id {
       my $line = shift;
       $line =~ /^KW\s+([A-Z]+)/i;
       $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.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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

bioperl-l@bioperl.org

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Ewan Birney

Also lorenz@ist.org, bosborne at alum.mit.edu

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: Specialist function to index Swissprot 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 : ref 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 Swissprot.pm
             Returns $1 from applying the regexp /^ID\s*(\S+)/
             or /^AC\s+([A-Z0-9]+)/ to the current line.
   Returns : ID string
   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    :