[Bioperl-l] loading yeast data failing...
Angshu Kar
angshu96 at gmail.com
Tue Jan 3 23:11:28 EST 2006
I apologize again Barry. But as Hilmar suggested it was about 2 lines of
code, I thought he had that piece which he could provide me with. I'm sorry
Hilmar. And I miised cc to bioperl in that mail and I wrote that mail much
earlier. But I apologize for that too.
May be my situation (Esp. time crunch) is driving me to behave this
ill-mannerdly. I'm sorry again. I am going to post no more to this community
till I'm well versed in perl,linux.
And I'm truly obliged by the support you people provided me with.
Thanks,
Angshu
On 1/3/06, Barry Moore <bmoore at genetics.utah.edu> wrote:
>
> 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 :
> > ----------------------------------------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
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