[Bioperl-l] Bio::Index::PDB

[Brian Osborne]

Shawn,

Both Bio::Index::Fasta and Bio::DB::Fasta allow you to stipulate the key you
want to use, as in:

my $inx = Bio::Index::Fasta->new( -filename   => $file_name . ".idx",
                                    -write_flag => 1 );
$inx->id_parser(\&get_id);
# make the index
$inx->make_index($file_name);

# where get_id() could look like:

# here is where the retrieval key is specified
  sub get_id {
     my $header = shift;
     $header =~ /^>.*\bsp\|([A-Z]\d{5}\b)/;
     $1;
  }

I've found this capability to be very useful myself.

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Shawn Hoon
Sent: Monday, October 13, 2003 9:18 PM
To: BioPerl List
Subject: [Bioperl-l] Bio::Index::PDB

Hi,
I wrote an indexer along the lines of the sequence index modules  for
PDB structure files.
Basically a lot of copying from Bio::Index::Fasta

Basically 2 modules added:

Bio::Index::AbstractStructure (which inherits from Bio::Index::Abstract)
Bio::Index::PDB

Usage:

     use Bio::Index::PDB;
     use strict;

     my $Index_File_Name = shift;
     my $inx = Bio::Index::PDB->new('-filename' => $Index_File_Name);
     my $out = Bio::Structure::IO->new('-format' => 'pdb','-fh' =>
\*STDOUT);

     foreach my $id (@ARGV) {
         my $struct= $inx->fetch($id); # Returns Bio::Structure object
         $out->write_structure($struct);
     }

Is this along the lines of how indexers are implemented? If so, I will
go ahead and commit them.


shawn

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