[Bioperl-l] rebuilding a genbank Bio Index

[Andreas Matern]

I have a Bio::Index::Genbank which has regretfully had its member files
updated.

I've been trying to rebuild the index like so: 
(N.B. this is exactly how I made the index in the first place)

use Bio::Index::GenBank;
my $Index_File_Name = "genbank";
my $inx = Bio::Index::GenBank->new('-filename' => $Index_File_name,
'-write_flag' => 'WRITE');
$inx->Make_index('/path/to/gbfile/file.seq');

and then trying to access it like so:

use Bio::Index::GenBank;
my $Index_File_Name = "genbank";
my $inx = Bio::Index::GenBank->new('-filename' => $Index_File_name);
@acc = $inx->get_all_primary_ids();
foreach my $acc (@acc) {
	//do fancy stuff here
}

But I still get errors like:

MSG: file 0 [/path/to/gbfile/file.seq ] has changed size 15543834 ->
165442561. This probably means you need to rebuild the index.

Am I missing something?  Is there some kind of 'update' or 'rebuild'
command I can't seem to find?
Any help is appreciated.

If it helps, I'm using the CVS version of bioperl (from Friday) on irix
with perl 5.6.0 under irix.

Thanks!

-Andreas
-- 


------------------
Andreas Matern
Bioinformatician
LION Bioscience Research, Inc.
141 Portland Street, 10th Floor
Cambridge, MA 02139

andreas.matern@lbri.lionbioscience.com
phone: (617) 245-5483
fax:   (617) 245-5499