[Bioperl-l] asn and Bio::TreeIO

[Lee Katz]

It looks like I get two options here for exporting.
http://i.imgur.com/TID5RiP.png

Both of them are viewable in MEGA5, so I export Newick (.dnd).  Most times
I can use BioPerl to look at the file.  However this particular version
gives me problems in BioPerl.

This is the current version giving me an error:
http://wikisend.com/download/657408/Listeria_2014_03_03_kmer_tree[1].asn
And the converted file using NCBI Workbench:
http://wikisend.com/download/598906/Listeria_2014_03_03_kmer_tree.asn.dnd

This is the TreeIO error.  Any hints on how to debug further?  Thank you!

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: parse error: expected ; or ) or ,

STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/local/share/perl/5.12.4/Bio/Root/Root.pm:472
STACK: Bio::TreeIO::NewickParser::parse_newick
/usr/local/share/perl/5.12.4/Bio/TreeIO/NewickParser.pm:195
STACK: Bio::TreeIO::newick::next_tree
/usr/local/share/perl/5.12.4/Bio/TreeIO/newick.pm:143
STACK: Bio::TreeIO::nexus::_parse /usr/local/share/perl/5.12.4/Bio/TreeIO/
nexus.pm:204
STACK: Bio::TreeIO::nexus::next_tree
/usr/local/share/perl/5.12.4/Bio/TreeIO/nexus.pm:129
STACK: main::printNewTree scripts/renameTreeNodes_v3.pl:64
STACK: main::main scripts/renameTreeNodes_v3.pl:30
STACK: scripts/renameTreeNodes_v3.pl:17
-----------------------------------------------------------


The while statement is line 64 which is where the error happens above.

  my $in=Bio::TreeIO->new(-file=>$inTree);
  my $out=Bio::TreeIO->new(); # stdout
  my %seen;
  my $i=0;
  while(my $tree=$in->next_tree){




On Mon, Mar 3, 2014 at 4:52 PM, Fields, Christopher J <cjfields at illinois.edu
> wrote:

>  Ick; no one really uses ASN1 outside of NCBI.  No XML output option?
>
>  chris
>
>  On Mar 3, 2014, at 3:50 PM, Lee Katz <lskatz at gmail.com> wrote:
>
>  It is from NCBI's genome workbench
> On Mar 3, 2014 4:40 PM, "Fields, Christopher J" <cjfields at illinois.edu>
> wrote:
>
>> Not that I’m aware of.  What was the source of the output?
>>
>> chris
>>
>> On Mar 3, 2014, at 2:32 PM, Lee Katz <lskatz at gmail.com> wrote:
>>
>> > Hi Bioperl, I was wondering if there is a way to read an asn file using
>> > Bio::Perl.  This is one of the files I want to look at.
>> >
>> > http://wikisend.com/download/372926/Listeria_2014_02_11_kmer_tree.asn
>> >
>> > --
>> > Lee Katz
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>


-- 
Lee Katz, Ph.D.