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

Sendu Bala bix at sendu.me.uk
Wed Aug 30 09:18:56 EDT 2006


Xianjun Dong wrote:
[...]
> my $protein =$seq->translate(-orf => 1,
>                              -complete => 1);
[...]
> 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.
[...]
> But this code is illustrated on Bioperl page:
> 
> http://www.bioperl.org/wiki/Bptutorial.pl#III.3.2_Translating

The tutorial (and wiki pages generally) refers to the latest release of 
Bioperl (1.5.1); I presume you are still using Bioperl 1.4? Look at the 
documentation for the version of Bioperl you are actually using:

http://doc.bioperl.org/releases/bioperl-1.4/Bio/PrimarySeqI.html#POD10

You'll see that in this version, PrimarySeqI doesn't take named arguments.


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