[Bioperl-l] basic questions

Chris Fields cjfields at uiuc.edu
Tue Jun 12 14:35:15 EDT 2007


Bio::Restriction::EnzymeCollection holds Bio::Restriction::Enzyme  
objects, each with its own name().  Using grouped methods like  
'$collection->cutters(6)' will retrieve a new EnzymeCollection  
containing all six-cutters from the original collection.  You should  
use one of the EnzymeCollection accessor methods to retrieve the  
enzyme that you wanted first or iterate through them all.  This works  
for me:

use Bio::Restriction::EnzymeCollection;
my $all_collection = Bio::Restriction::EnzymeCollection->new();
my $six_cutter_collection = $all_collection->cutters(6);
for my $enz ($six_cutter_collection->each_enzyme){
    print $enz->name,"\t",$enz->site,"\t",$enz->overhang_seq,"\n";
}

chris

On Jun 12, 2007, at 1:11 PM, L Xu wrote:

> Thank you very much, it did make the script advanced a bit but I  
> got the following error:
>
> C:\~Scripts>perl t9.pl
> Can't locate object method "name" via package  
> "Bio::Restriction::EnzymeCollectio
> n" at t9.pl line 5, <DATA> line 532.
>
> I checked the documentation , there is no "name" method for the  
> package. Thanks.



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