[Bioperl-l] extract info from .game.xml

[Sheldon McKay]

Hi Tuan,

Your game XML file contains only sequence and computational_analysis 
elements, with no annotation elements.  Unfortunately lack of 
annotations is fatal and computational analysis features are not 
supported in the bioperl parser.  Lack of annotations does not 
necessarily need to be fatal, though.  I will see what I can do about 
that.

Sheldon

On Jul 11, 2005, at 12:05 PM, Tuan A. Tran wrote:

> Hi Sheldon,
>
> Thanks very much for your email. Yes, I am still interested in doing 
> that.
> It is quite a while ago so I don't remember what I might have done
> wrong. Anyway, I seem to recall that in attached data file, there is
> not any 'annotation' anywhere. I have not checked since then. I just
> downloaded the attached file from flybase.org.
>
>  I hope that you can help me to figure out.
>
>  Sincerely,
>  Tuan
>
>
> On 7/7/05, Sheldon McKay <mckays at cshl.edu> wrote:
>> Hi,
>>
>> Sorry for taking so long to reply.  If you are still interested in
>> doing this, could you send me the file you are trying to parse and i
>> will see if I can figure out what is wrong?
>>
>> Thanks,
>> Sheldon
>>
>>
>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>> Sheldon McKay, PhD
>> Cold Spring Harbor Laboratory
>> 1 Bungtown Road
>> Cold Spring Harbor, NY 11724
>> On Jun 14, 2005, at 8:03 PM, Tuan A. Tran wrote:
>>
>>> Hi,
>>>
>>> I am trying to extract some information from a file filename.game.xml
>>> (I got this file from flybase.org). I wrote a simple script to test
>>> it. However, I keep getting the following message
>>>
>>> ------------- EXCEPTION  -------------
>>> MSG: No annotations
>>> STACK Bio::SeqIO::game::gameHandler::load
>>> /usr/local/share/perl/5.8.4/Bio/SeqIO/game/gameHandler.pm:121
>>> STACK Bio::SeqIO::game::_getseqs
>>> /usr/local/share/perl/5.8.4/Bio/SeqIO/game.pm:156
>>> STACK Bio::SeqIO::game::next_seq
>>> /usr/local/share/perl/5.8.4/Bio/SeqIO/game.pm:101
>>> STACK toplevel fetchseq_game_xml.pl:64
>>>
>>> I have no idea why. Can anyone help?
>>> Thanks in advance,
>>> TAT
>>>
>>> ---------------------------------
>>> My simple script is
>>>
>>> #!/usr/local/lib/perl
>>>
>>> use strict;
>>>
>>> sub NULL () {0};
>>>
>>> use Bio::Seq;
>>> use Bio::SeqIO;
>>> #use Bio::SeqIO::game;
>>> #use Bio::Annotation;
>>> use Bio::SearchIO;
>>> use Bio::AlignIO;
>>> use Bio::SimpleAlign;
>>> use Bio::LocatableSeq;
>>> use Bio::Tools::Run::StandAloneBlast;
>>> use Bio::Tools::Run::Alignment::Clustalw;
>>> use Getopt::Long;
>>> use Bio::DB::GenBank;
>>> use Bio::DB::Flat::BDB;
>>> #use Bio::Index::GenBank;
>>> use Bio::Index::Fasta;
>>> use Bio::SeqFeature::Generic;
>>> use DBI;
>>>
>>>
>>> my $infile = shift;
>>> my $in = Bio::SeqIO->new( -file=> $infile, -format=>'game');
>>>
>>> while (my $query = $in->next_seq() ) {
>>>
>>>       print $query->id,"\n";
>>> }
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
> <3R_27900000_28200000.game.xml.gz>