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

[Chris Fields]

One can also look here:

http://doc.bioperl.org/bioperl-live/

I think that syncs to the github.  Thought, truthfully, I tend to simply perldoc it, or use search.cpan.org/search.metacpan.org (Chrome makes this easy).  MetaCPAN is nice but the search is still a little flaky.

http://search.cpan.org/perldoc?Bio::Restriction::Analysis
http://search.metacpan.org/#/showpod/Bio::Restriction::Analysis

chris

On Jul 8, 2011, at 9:56 AM, Kevin Brown wrote:

> Please keep replies on the list.
> 
> Yes, that is the wrong place to look as that is BioPerl v1.4 (notice the path) whereas the software you are trying to use is v1.6 (hopefully 1.6.9). So, those docs aren't "out of date" so much as they belong to a different version of the software.
> 
> -----Original Message-----
> From: Mark Nadel [mailto:nadel at nabsys.com]
> Sent: Thu 7/7/2011 2:50 PM
> To: Kevin Brown
> Subject: Re: [Bioperl-l] position method in Bio::Restriction::Analysis
> 
> I got the information from
> http://doc.bioperl.org/releases/bioperl-1.4/Bio/Restriction/Analysis.html#POD5.
> Is this the wrong place to be looking? I accidently said position instead of
> positions, but that is not the problem.
> 
> On Thu, Jul 7, 2011 at 5:26 PM, Kevin Brown <Kevin.M.Brown at asu.edu> wrote:
> 
>> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
> 
> 
> 
> -- 
> *Mark Nadel*
> *Principal Scientist
> *
> NABsys Inc.
> 60 Clifford Street
> Providence, RI  02903
> 
> Phone   401-276-9100 x204
> Fax 401-276-9122
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l