[Bioperl-l] Indexing est fasta file.

[Brian Osborne]

Ivan,

My Google search says:
On failure, the tie call returns an undefined value and probably sets $! to
contain the reason the file could not be tied.
sdbm store returned -1, errno 22, key "..." at ...
This warning is emmitted when you try to store a key or a value that is too
long. It means that the change was not recorded in the database. See BUGS
AND WARNINGS below.
Your key can't be too long - is there something unusual about this
particular sequence or "value"?

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 Ivan Sendin
Sent: Thursday, July 03, 2003 3:47 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Indexing est fasta file.

Hi,

I'm trying to make an index on est file, but
when I run my script I got this error:

sdbm store returned -1, errno 22, key "6861423" at
/usr/local/lib/perl5/site_perl/5.8.0/Bio/Index/Abstract.pm line 713, <FASTA>
line 22096655.


The script is very simple:

...
 my $inx = Bio::Index::Fasta->new(
                                   -filename => $Index_File_Name,
                                   -write_flag => 1
                                  );
  $inx->id_parser(\&parse_ncbi_id);
  $inx->make_index($fasta);
}

sub parse_ncbi_id {
  my @retvals;
  my $p = $_[0];
  if( $p =~ /^>(\S+)/ ) {
    my $val = $1;
    push @retvals, $val;
    while ( $p =~/gi\|(\d*)/g) {
      push(@retvals,$1);
    }
  }
  return @retvals;
}


Anybody knows what is wrong?

The size of est file (11077527557 bytes) is a issue?


Thanks,


Ivan Sendin

__________________________________
Do you Yahoo!?
SBC Yahoo! DSL - Now only $29.95 per month!
http://sbc.yahoo.com
_______________________________________________
Bioperl-l mailing list
Bioperl-l at portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l