[Bioperl-l] Bioperl objects and subroutines

Stefan Kirov skirov at utk.edu
Wed May 12 10:43:54 EDT 2004

Hi Jonathan,
I believe what you should do is:

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

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

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
>$reference = \$seqobject;
>And within the subroutine attempt to access like:
>$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.
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

More information about the Bioperl-l mailing list