[Bioperl-l] Indexing est fasta file.

[Brian Osborne]

Ivan,

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.

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

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: 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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=====
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 Ivan da Silva Sendin  -   Bioinformatics
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