[Bioperl-l] Indexing est fasta file.

[Ivan Sendin]

Brian,

> Puzzling. One thing I'd try if this had happened to me would be to 
switch
> from SDBM to DB_File as the indexing method. In order to do this 
you'll have
> to install DB_File (from RPM say, or from www.sleepycat.com) and then
> install the DB_File Perl module. This doesn't sound like a problem 
with
> Bioperl per se, it seems like a problem with SDBM, that's my guess.
 
I'll try DB_File.


> One question though: why do you say that the keys are both
> "gi|6861423|gb|AW357480.1|AW357480" and "6861423" for that sequence? 
Are you

Because there are old scripts that search for
"gi|6861423|gb|AW357480.1|AW357480" and new scripts using only gi...
I will fix it someday.

I've tried index est file again using "gi" as key and the error
happened again:

15944439
15944440
sdbm store returned -1, errno 22, key "15944440" at
/usr/local/lib/perl5/site_perl/5.8.0/Bio/Index/Abstract.pm line 713, 
<FASTA>
line 63813394.

> using the idparser() method to specify /gi\|(\d+)/ as the key? You 
might
> want to show us the code, this is often illuminating.

The code is in the end of first mail... some "Page Down"
from here...


Thanks,

Ivan

> -----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: Friday, July 04, 2003 8:35 AM
> To: bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] Indexing est fasta file.
> 
> 
> --- Brian Osborne <brian_osborne at cognia.com> wrote:
> > 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,
> 
> There is not unusual with this sequence.
> I runned the script again, printing some debug info:
> ......
> gi|6861420|gb|AW357477.1|AW357477 6861420
> gi|6861421|gb|AW357478.1|AW357478 6861421
> gi|6861422|gb|AW357479.1|AW357479 6861422
> gi|6861423|gb|AW357480.1|AW357480 6861423
> 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 keys for the last sequence are "gi|6861423|gb|AW357480.1|AW357480"
> and "6861423".
> 
> 
> Ivan
> 
> 
> 
> 
> > 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
> >
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> 
> =====
> ------------------------------------------------------------
>  Ivan da Silva Sendin  -   Bioinformatics
>  Raw IP,TCP & UDP with Java: http://jpacket.sourceforge.net
>                                Campinas - Brasil
> ------------------------------------------------------------
> 
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