[Bioperl-l] Error while running load_seqdatabase.pl

George Heller george.heller at yahoo.com
Sat Jan 27 21:31:56 EST 2007


Hi Hilmar, 
   
  I tried the lookup and noupdate options, and also made changes to the SeqProcessor.pm package for the accession, 
  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, $seq) = @_;
  my @ids = split(/|/,$seq->display_id);
  $seq->accession_number($ids[0]);
  return ($seq);
}
1;
  I invoke the load_seqdatabase.pl as, 
  perl load_seqdatabase.pl -host localhost -dbname usda-06 -format fasta -dbuser postgres -driver Pg --lookup --noupdate --pipeline="SeqProcessor::Accession" maize_pep.fasta
Loading maize_pep.fasta ...
  I get the error,
-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were ("FGENESHT0000021||AC155633|113788|114708|-1","FGENESHT0000021||AC155633|113788|114708|-1","FGENESHT0000021||AC155633|113788|114708|-1","","0","") FKs (1,<NULL>)
ERROR:  value too long for type character varying(40)
---------------------------------------------------
Could not store FGENESHT0000021||AC155633|113788|114708|-1:
------------- EXCEPTION  -------------
MSG: error while executing statement in Bio::DB::BioSQL::SeqAdaptor::find_by_unique_key: ERROR:  current transaction is aborted, commands ignored until end of transaction block
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:951
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:205
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
STACK Bio::DB::Persistent::PersistentObject::store /home/akar/local/perl//Bio/DB/Persistent/PersistentObject.pm:272
STACK (eval) load_seqdatabase.pl:620
STACK toplevel load_seqdatabase.pl:602
--------------------------------------
 at load_seqdatabase.pl line 633
  As far as I gather, this error shouldnt appear as we are filtering out the accession as only the first code that appears. Ideas?
   
  George.


Hilmar Lapp <hlapp at gmx.net> wrote:
  George,

I don't know you create the FASTA file, but that's probably where the 
root cause is. Based on the message:

> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values 
> were ("FGENESHT0000001||AC155633|570|4400|1","FGENESHT0000001|| 
> AC155633|570|4400|1","FGENESHT0000001||AC155633|570|4400| 
> 1","","0","") FKs (1,)
> ERROR: duplicate key violates unique constraint 
> "bioentry_accession_key"
> ---------------------------------------------------

the identifier and accession number are set, so your SeqProcessor 
scriptlet was executed (otherwise you'd also have seen a dynamic 
loading error it e.g. you perl class could be not be found or loaded 
by perl). If you still receive the duplicate key violation, then it 
can only mean that indeed a sequence with the exact same accession 
number was in the database already.

There are different possibilities for why: you may have loaded the 
same file before (use --lookup and related switches if you want to 
update existing sequences), or your FASTA file contains multiple 
sequences with the same ID, or you have a sequence with the same ID 
in different FASTA files, if you are loading from more than one file. 
In either of the two latter cases, you will need to find a way to 
disambiguate the IDs.

BTW you also want to consider to parse the concatenated ID 
'FGENESHT0000001||AC155633|570|4400|1' apart into its component IDs, 
and then use only one component. For example:

my @ids = split(/|/,$seq->display_id);
$seq->accession_number($ids[0]);

Obviously, this will only make for a nicer accession number, and not 
solve your duplicate ID problem, as the latter is in the file(s) you 
load.

-hilmar

On Jan 25, 2007, at 8:51 PM, George Heller wrote:

> Hi Hilmar,
>
> I still seem to be having problems loading my fasta file. I wrote a 
> new package, SeqProcessor.pm as below,
>
> 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);
> }
> 1;
> I have this file SeqProcessor.pm in my home directory, and I have 
> set the PERL5LIB variable accordingly. When I run load_seqdatabase.pl,
>
> perl load_seqdatabase.pl -host localhost -dbname biodb -format 
> fasta -dbuser postgres -driver Pg -- 
> pipeline="SeqProcessor::Accession" maize_pep.fasta
>
> I still get the error,
>
> Loading maize_pep.fasta ...
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values 
> were ("FGENESHT0000001||AC155633|570|4400|1","FGENESHT0000001|| 
> AC155633|570|4400|1","FGENESHT0000001||AC155633|570|4400| 
> 1","","0","") FKs (1,)
> ERROR: duplicate key violates unique constraint 
> "bioentry_accession_key"
> ---------------------------------------------------
> Could not store FGENESHT0000001||AC155633|570|4400|1:
> ------------- EXCEPTION -------------
> MSG: error while executing statement in 
> Bio::DB::BioSQL::SeqAdaptor::find_by_unique_key: ERROR: current 
> transaction is aborted, commands ignored until end of transaction 
> block
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key / 
> home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:951
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key / 
> home/akar/local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:855
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /home/akar/ 
> local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:205
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /home/akar/ 
> local/perl//Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
> STACK Bio::DB::Persistent::PersistentObject::store /home/akar/local/ 
> perl//Bio/DB/Persistent/PersistentObject.pm:272
> STACK (eval) load_seqdatabase.pl:620
> STACK toplevel load_seqdatabase.pl:602
> --------------------------------------
> at load_seqdatabase.pl line 633
> Is there something I am missing?
>
> Thanks!
> George.
>
>
> Hilmar Lapp wrote:
> 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 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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-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
===========================================================







 
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