[Bioperl-l] loading yeast data failing...

[Barry Moore]

Angshu-

Have you not been listening to anything that has been written to you on
this list.  The Bioperl community has been amazingly patient with your
questions over the last several months, and many have told you time and
time again that you should think before you post. Less than an hour ago
Hilmar and I both suggested ways that you could try to solve your own
problem, and now you are back asking Hilmar to write code for you?
Unbelievable.  Asking Hilmar to write your code for you is VERY
UNACCEPTABLE!!!  If you need to have someone write your code for you or
tutor you in the basics of Perl and Linux (and I think you do) then you
need to hire them.  I can recommend some skilled contract programmers if
you need to hire one.  This list welcomes beginners, but you are
expected to put forth some effort at trying to solve problems yourself
first.  Your brazen disregard for the etiquette of open source mailing
lists suggests to me that you should not trouble the Bioperl community
with further questions until you have at least a basic command of Perl
and Linux and a willingness to try things yourself first.  Get a copy of
Programming Perl and read it!  Get a copy of Object Oriented Perl and
read it!  Get a copy of any Linux manual and read it!  And most
important of all, just write code and try it - you won't break the
computer!

Barry

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
> bounces at portal.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Tuesday, January 03, 2006 2:36 PM
> To: bioperl-l
> Subject: Fwd: [Bioperl-l] loading yeast data failing...
> 
> ---------- Forwarded message ----------
> From: Angshu Kar <angshu96 at gmail.com>
> Date: Jan 3, 2006 1:31 PM
> Subject: Re: [Bioperl-l] loading yeast data failing...
> To: Hilmar Lapp <hlapp at gmx.net>
> 
> 
> Hi Hilmar,
> 
> If you have some time, could you please write those 2 lines for me? I
> just have no clue about it. After that I think I've to rebuild the
> package. Am I right?
> 
> Here is the accessor.pm:
> 
> use strict;
> use vars qw(@ISA);
>  use lib '/home/akar/local/perl/';
> 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);
>  }
> 
> 
> Thanks,
> Angshu
> 
> 
> On 1/3/06, Hilmar Lapp <hlapp at gmx.net> wrote:
> > You could do that but first that puts you out of sync with the
> > official schema, and second if you look at the value it isn't really
> > an accession number anyway that's causing the problem but rather a
> > concatenation of identifiers, accession numbers, and namespace
> > acronyms. Since you're using a custom SeqProcessor anyway already
why
> > don't you just add a line or two of code that parses the display_id
> > value into the accession and identifier? (for instance, the token
> > between two '|' characters following the token 'gb')
> >
> >    -hilmar
> >
> > On 1/3/06, Angshu Kar <angshu96 at gmail.com > wrote:
> > > Hi,
> > >
> > > Could you please help me resolve the follwoing error?
> > >
> > > I run:
> > >
> > > ./load_seqdatabase.pl --dbname=USBA --dbuser=postgres
--format=fasta
> > > --driver=Pg --pipeline="SeqProcessor::Accession" yeast_nrpep.fasta
> > >
> > > The error:
> > >
> > > Loading yeast_nrpep.fasta ...
> > >
> > > -------------------- WARNING ---------------------
> > > MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values
> were
> > >
>
("gi|4261605|gb|AAD13905.1|S58126_11111111111111","gi|4261605|gb|AAD1390
5.
>
1|S58126_11111111111111","gi|4261605|gb|AAD13905.1|S58126_11111111111111
",
> "Unknown
> > > [Saccharomyces cerevisiae]","0","") FKs (19,<NULL>)
> > > ERROR:  value too long for type character varying(40)
> > > ---------------------------------------------------
> > > Could not store gi|4261605|gb|AAD13905.1|S58126_11111111111111:
> > > ------------- 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:621
> > > STACK toplevel ./load_seqdatabase.pl:604
> > >
> > > --------------------------------------
> > >
> > >  at ./load_seqdatabase.pl line 634
> > >
> > > Should I change the field lengths for accession, name and
identifier
> to some
> > > value >40 in the bioentry table?  What  should I change it to?
> > >
> > > Thanks,
> > > Angshu
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > >
> >
> >
> > --
> > ----------------------------------------------------------
> > : Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
> > ----------------------------------------------------------
> >
> 
> 
> 
> --
> ----------------------------------------------------------
> : Hilmar Lapp -:- San Diego, CA -:- hlapp at gmx dot net :
> ----------------------------------------------------------
> 
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