[Bioperl-l] Restriction Enzyme Analysis

[Mark Nadel]

Let me preface this question by saying that, after following various online
sets of instructions, I was unable to "install" bioperl on my Mac.
However, by simply copying Bio into a Perl directory, I have some limited
functionality. I don't know if this is an installation issue, or if there is
a problem with the module, or most probably, with my understanding of the
module.

Here is a short script to illustrate the issue:

use strict;

use Bio::Restriction::EnzymeCollection;

my $re=Bio::Restriction::Enzyme->new

      (-enzyme=>'EcoRI', -seq=>'G^AATTC');

my $a = $re->name();

print "The name is $a\n";



my $all_collection = Bio::Restriction::EnzymeCollection->new();

my $x = $all_collection->available_list();

print "the available list is $x\n";

my $six_cutter_collection = $all_collection->cutters(6);

my $y = $six_cutter_collection->available_list();

print "the available list is $y\n";



for my $enz ($six_cutter_collection){

   print $enz->name,"\t",$enz->site,"\t",$enz->overhang_seq,"\n";

   # prints name, recognition site, overhang

}


The output is

The name is EcoRI

the available list is 532

the available list is 266

Can't locate object method "name" via package
"Bio::Restriction::EnzymeCollection" at
/Users/marknadel/Documents/workspace/adHoc/bioperl_restriction_digest.plline
22, <DATA> line 532.

I would seem that some of this is working, but the last part, taken directly
from the HOWTO, is not.

If someone reading this list can help me with this, I would be most
grateful.

Thanks in advance,

Mark Nadel