[Bioperl-l] Error while running load_seqdatabase.pl

Hilmar Lapp hlapp at gmx.net
Sun Jan 14 12:05:19 EST 2007


Hi George, sorry for the sluggish response, I was tied up during the  
week. This is also why you always want to keep the thread on the list.

Perl is an interpreted language, so no compilation is necessary. The  
only thing you need to do is have the package in a place where perl  
can find it. The simplest way to achieve this is by setting the  
PERL5LIB environment variable:

	$ export PERL5LIB=/where/you/put/your/perl/package

or if PERL5LIB was set already, you'd append it:

	$ export PERL5LIB=${PERL5LIB}:/where/you/put/your/perl/package

I do assume that you didn't really add your code to the SeqAdaptor.pm  
package - there is no necessity for nor benefit from that, and at  
worst (and quite likely) perl won't be able to find the package. Note  
that there is plenty of documentation for how to write packages for  
perl and how to make them accessible to perl.

Hth,

	-hilmar

On Jan 8, 2007, at 11:52 PM, George Heller wrote:

> Hi Hilmer.
>
> Thanks so much for the response. As I am new to Bioperl, I have  
> another question.
>
> I have made the changes as suggested by you, and have added the  
> code below to the SeqAdaptor.pm script.
>
> package SeqProcessor::Accession;
> use strict;
> use vars qw(@ISA);
> use Bio::Seq::BaseSeqProcessor;
> use Bio::SeqFeature::Generic;
>
> @ISA = qw(Bio::Seq::BaseSeqProcessor);
>
> sub process_seq
> {
>   my ($self, $seq) = @_;
>   $seq->accession_number($seq->display_id);
>   return ($seq);
> }
>
> Now that I have done my changes, do I need to compile or something  
> for the changes to reflect? If so, can you please let me know the  
> command for the same, or direct me to any lin that has  
> documentation for the same?
>
> Thanks so much for the help.
> George.
>
> Hilmar Lapp <hlapp at gmx.net> wrote:
> George,
>
> this is almost certainly caused by using FASTA format and bioperl's
> treatment of it. I am guilty of not having written a FAQ yet for
> Bioperl-db, as this would certainly be there.
>
> Specifically, the Bioperl fasta SeqIO parser (load_seqdatabase.pl
> uses Bioperl to parse sequence files) does not extract the accession
> number from the description line of the fasta sequence, and instead
> sets the accession_number property if sequence objects it creates to
> "unknown". Since there is a unique key constraint on
> (accession,version,namespace) the second sequence loaded will raise
> an exception as it will violate the constraint.
>
> The simplest way to deal with this is to write a SeqProcessor that
> massages the accession_number appropriately and then supply the
> module to load_seqdatabase.pl using the --pipeline command line  
> switch.
>
> There are several examples for how to do this in the email archives.
> See for example this thread on the Biosql list:
>
> http://lists.open-bio.org/pipermail/biosql-l/2005-August/000901.html
>
> with two links to examples, and Marc Logghe gives another one in the
> thread itself.
>
> Hth,
>
> -hilmar
>
> On Jan 8, 2007, at 3:17 PM, George Heller wrote:
>
> > Hi all.
> >
> > I am new to Bioperl and am trying to run the load_seqdatabase.pl
> > script to load sequence data from a file into Postgres database. I
> > am invoking the script through the following command:
> >
> > perl load_seqdatabase.pl -host localhost -dbname biodb06 -format
> > fasta
> > -dbuser postgres -driver Pg
> >
> > I am getting the following error:
> >
> > -------------------- WARNING ---------------------
> > MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values
> > were ("FGENES
> > HT0000001||AC155633|570|4400|1","FGENESHT0000001||AC155633|570|4400|
> > 1","unknown"
> > ,"","0","") FKs (1,)
> > ERROR: duplicate key violates unique constraint
> > "bioentry_accession_key"
> > ---------------------------------------------------
> > Could not store unknown:
> > ------------- EXCEPTION -------------
> > MSG: error while executing statement in
> > Bio::DB::BioSQL::SeqAdaptor::find_by_uni
> > que_key: ERROR: current transaction is aborted, commands ignored
> > until end of t
> > ransaction block
> > STACK
> > Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/
> > lib/perl
> > 5/site_perl/5.8.5/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:948
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /
> > usr/lib/perl5
> > /site_perl/5.8.5/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/
> > perl5/site_perl/5
> > .8.5/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:203
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/
> > site_perl/5.
> > 8.5/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> > STACK Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/
> > site_perl/5.8.
> > 5/Bio/DB/Persistent/PersistentObject.pm:271
> > STACK (eval) load_seqdatabase.pl:620
> > STACK toplevel load_seqdatabase.pl:602
> > --------------------------------------
> > at load_seqdatabase.pl line 633
> >
> > Can anyone tell me how I can correct this error and get my script
> > running? Thanks!!!
> >
> > George.
> >
> >
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> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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