[Bioperl-l] Indexing est fasta file.

[Ivan Sendin]

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

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