[Bioperl-l] asn and Bio::TreeIO

[Hilmar Lapp]

Have you tried deleting the trailing empty line and see whether that
changes anything? You could also try to specify the format expressly as
newick. (It looks like it's picking NEXUS by default.)

The error is because of a format mismatch between what's in the file and
what the Newick parser expects. Since there are so many characters in the
OTU labels that many programs would balk at, it's hard to see where the
mismatch might be.

   -hilmar


On Mon, Mar 3, 2014 at 5:14 PM, Lee Katz <lskatz at gmail.com> wrote:

> Just a little bigger scope of my script.  $inTree is the filename of the
> input dnd file.
>
> sub printNewTree{
>   my($inTree,$map,$settings)=@_;
>   my $d=$$settings{delimiter} || die "ERROR: there is no
> delimiter\n".usage();
>   my $suffix=$$settings{suffix};
>   my $in=Bio::TreeIO->new(-file=>$inTree);
>   my $out=Bio::TreeIO->new(); # stdout
>   my %seen;
>   my $i=0;
>   while(my $tree=$in->next_tree){
>     for my $node($tree->get_nodes){
>       #if ($i++>100){
>       #  logmsg "DEBUG";
>       #  last;
>       #}
>       my $oldid=$node->id || "";
>
>
> And there is a ton more code below this that is probably irrelevant.
>
>
>
>
> On Mon, Mar 3, 2014 at 5:12 PM, Lee Katz <lskatz at gmail.com> wrote:
>
> > 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.
> >
>
>
>
> --
> Lee Katz, Ph.D.
>
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>



-- 
Hilmar Lapp -:- lappland.io