[Bioperl-l] problem with $seq_obj->translate()

Xianjun Dong Xianjun.Dong at bccs.uib.no
Wed Aug 30 07:58:10 EDT 2006


Hi,

I have problem when running the following code:

-------------------------------------------------------
my $seq=Bio::Seq->new(-seq =>"tttttatgccctaggggg",
                      -id  => "test1");
my $protein =$seq->translate(-orf => 1,
                             -complete => 1);
print $protein->seq();
-------------------------------------------------------

The error msg is:

Argument "-complete" isn't numeric in numeric eq (==)
at /usr/lib/perl5/site_perl/5.8.5/Bio/PrimarySeqI.pm line 533.

I don't know why. The same case if I change to use other options, like
"-codontable_id => 2, -orf =>1". Anyway, if I use more than 1 options in
translate() function, it will occur some error, like

Argument "-orf" isn't numeric in numeric eq (==)
at /usr/lib/perl5/site_perl/5.8.5/Bio/PrimarySeqI.pm line 533.

But this code is illustrated on Bioperl page:

http://www.bioperl.org/wiki/Bptutorial.pl#III.3.2_Translating

Could you help me?

Thanks


-- 
Xianjun Dong 
PhD Student 
Computational Biology Unit 
Bergen Center for Computational Science 
University of Bergen
Høyteknologisenteret, Thormøhlensgate 55 
N-5008 Bergen,Norway. 
Webpage: http://www.ii.uib.no/~xianjund/ 
MSN: sterding at hotmail.com
Phone No: +47 - 55584354 (office)
          +47 - 47361688 (mobile)
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