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

[chen li]

Hi Angshu,

As I told you before Dr.Barry Moore,Dr. Hilmar Lapp,
and Dr. Jason Stajich (and others) are professors in
the Dept of Computer Science (or something like that).
They are pretty busy and spend their free time to host
this mailing list without any reimbursements.  You ask
them to write the code for you just like asking your
professor to do the job for you. This is the reason
why you get your ass kicked. You might get around your
problem by doing some research on google, or search
the mailing list to see if the same question is asked
before, or search  similar mailing lists. But anyway
you should do some reading and write you code first
and run it. Just try and it is very painful for a
beginer but it is worth.

Good luck,
 
Li

--- 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
> > > >
> > > >
> _______________________________________________
> 
=== message truncated ===



		
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