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Barry Moore | 4 Jan 2006 03:33
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RE: loading yeast data failing...

Angshu-

You should read the following documents carefully before asking more
questions like this one, this is yet another example that demonstrates
that you ask questions before you try to solve the problem yourself.  Do
you have a copy of Programming Perl sitting next to you on the desk?  If
not you should, and it should be tattered and worn before you hit the
list with basic questions like that.  Now try these documents and the
suggestions below, repent of you ways and good luck.

http://www.catb.org/~esr/faqs/smart-questions.html

http://chicago.pm.org/meetings/20031202/perl-debug.txt

http://debugger.perl.org/580/perldebug.html

Now to get you headed on you way for this problem, specifically, what
you want to know about the perl debugger for this issue is:

You can run it like this:

perl -d your_script.pl

You can burrow into your code to the module in question like this:

c Path::To::Your::accessor::process_seq

Once there you can step through code with n or s.

Finally, you can look at varibles (and objects and methods called on
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Marc Logghe | 4 Jan 2006 09:03

RE: loading yeast data failing...

Hi Angshu,
Allow me to make a remark before you run into more (coding and other)
troubles.

> > > 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( <at> ISA);
> > >  use lib '/home/akar/local/perl/';
> > > use Bio::Seq::BaseSeqProcessor;
> > > use Bio::SeqFeature::Generic;
> > >
> > >  <at> ISA = qw(Bio::Seq::BaseSeqProcessor);
> > >
> > >  sub process_seq
> > > {
> > >   my ($self, $seq) =  <at> _;
> > >    $seq->accession_number($seq->display_id);
> > >   return ($seq);
> > >  }
> > >
> > > > > I run:
> > > > >
> > > > > ./load_seqdatabase.pl --dbname=USBA --dbuser=postgres
> > --format=fasta
> > > > > --driver=Pg --pipeline="SeqProcessor::Accession"
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Barry Moore | 4 Jan 2006 04:46
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RE: loading yeast data failing...

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
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chen li | 4 Jan 2006 06:08
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RE: loading yeast data failing...

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
(Continue reading)

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Angshu Kar | 4 Jan 2006 05:11
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Re: loading yeast data failing...

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
(Continue reading)

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Gmane