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:

            

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

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    :
            
          

cpanm BioPerl

perl -MCPAN -e shell
install BioPerl