[Bioperl-l] asn and Bio::TreeIO
Lee Katz
lskatz at gmail.com
Tue Mar 4 14:58:35 UTC 2014
Thank you for the suggestion. I did not have an second line to delete. So
I added a new one anyway! In both forms, the dnd did not work. I did
however notice ^M at the end of the original dnd file (using vim) and so I
ran dos2unix on it too, but it did not help either.
I also tried explicitly defining the format just in case because it might
have been trying the wrong format, but it still gives a similar error:
my $in=Bio::TreeIO->new(-file=>$inTree,-format=>"newick");
------------- 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: main::printNewTree scripts/renameTreeNodes_v3.pl:64
STACK: main::main scripts/renameTreeNodes_v3.pl:30
STACK: scripts/renameTreeNodes_v3.pl:17
On Mon, Mar 3, 2014 at 7:07 PM, Hilmar Lapp <hlapp at drycafe.net> wrote:
> 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.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> Hilmar Lapp -:- lappland.io
>
>
--
Lee Katz, Ph.D.
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