[Bioperl-l] position method in Bio::Restriction::Analysis

[Kevin Brown]

Try using the Deobfuscator. Not sure where you got the information that Restriction::Enzyme has a position method, but according to the docs for Bioperl-live it doesn't.

http://bioperl.org/cgi-bin/deob_interface.cgi?Search=Search&module=Bio%3A%3ARestriction%3A%3AEnzyme&sort_order=by+method&search_string=Bio%3A%3ARestriction

I think you're wanting the overhang_seq method which returns a Bio::Locatable object.


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org on behalf of Mark Nadel
Sent: Thu 7/7/2011 2:04 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] position method in Bio::Restriction::Analysis
 
I am having trouble using the position method, and no sample code is
included in the documentation.

Here is my script:
*
*
*

use strict;

use Bio::Restriction::EnzymeCollection;

use Bio::Restriction::Analysis;

use Bio::DB::GenBank;

use Bio::Seq;

use Bio::SeqIO;

use Bio::Seq::RichSeq;

use Bio::Tools::SeqStats;



my $accension_number = 'M77815';  ##'U00096.2';


my $outputFile = "/Users/marknadel/Documents/UniqueCutters".$
accension_number.".txt";


open OUT, ">$outputFile" or die "Can't open $outputFile";


my $db = Bio::DB::GenBank->new();


my $seq = $db->get_Seq_by_acc($accension_number);


print ">";

print $seq->desc();

print "\tThe sequence is circular:";

print $seq->is_circular();



print "\n";


my $ra = Bio::Restriction::Analysis->new(-seq=>$seq);


my $all_cutters = $ra->cutters;


my $uniqe = $ra->unique_cutters;





foreach my $enz ($uniqe->each_enzyme()){

print $enz->name();

print OUT $enz->name();

print "\t";

print OUT "\t";

    my @cutpoint = $enz->position();

    #print $cutpoint;

   # print OUT $cutpoint;





   }

print "\n";

    print OUT "\n";

    close OUT;

---------------------


and here is the output:


>M13mp18 phage cloning vector. The sequence is circular:1

AasI Can't locate object method "position" via package
"Bio::Restriction::Enzyme"
at /Users/marknadel/Documents/workspace/adHoc/unique_cutters.pl line 42,
<DATA> line 532.


I had a similar problem before with another method  in this package and
someone was kind enough to give me the exact syntax.

Thanks in advance,

Mark

*

-- 
*Mark Nadel*
*Principal Scientist
*
NABsys Inc.
60 Clifford Street
Providence, RI  02903

Phone   401-276-9100 x204
Fax 401-276-9122
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