[Bioperl-l] Bioperl objects and subroutines

[Brian Osborne]

Stefan,

> If you have
> a debugger like ptkdb (perl -d:ptkdb somescript.pl) take a look at what
> actually $seq contains.

Or use the "x" command in the perl debugger:

>perl -d <script>

Followed by:

<DB>x $seq


Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Stefan Kirov
Sent: Wednesday, May 12, 2004 10:44 AM
To: bmb9jrm at bmb.leeds.ac.uk
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Bioperl objects and subroutines

Hi Jonathan,
I believe what you should do is:

my $seq=new Bio::Seq (-seq=>'acagtcgatgc', -id=>'blabla');
somesub($seq);

sub somesub {
my $seq=shift;
print $seq->id;
}
And I think you should not be blessing a blessed reference. If you have
a debugger like ptkdb (perl -d:ptkdb somescript.pl) take a look at what
actually $seq contains. Also depending on how you call the sub, @_[0]
may contain the package name or other data. @_ is a tricky bussiness, be
carefult with it. Caling &somesub makes current @_ available to somesub
(which I don't know what is in your script). Try subroutine($seqobject)
instead like in the above example.

Hope this helps
Stefan

Jonathan Manning wrote:

>Hi all,
>
>Sorry if this seems more like a general perl question, but I can't find
>the answer I need in my books.
>
>How do I pass an object (specifically a Bio::Seq object) to a perl
>subroutine? I thought object variables were references anyway, but
>passing those variables didn't work. At the moment I pass a reference
>like:
>
>$reference = \$seqobject;
>&subroutine($reference);
>
>And within the subroutine attempt to access like:
>
>$sequence = bless @_[0];
>
>But this doesn't work either, and I can't access the object methods.
>
>Obviously I'm no perl veteran, and don't really know how to do it.
>Thanks in advance for any help.
>
>Jon
>
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