[Bioperl-l] Bio::FeatureIO::gff bug?

Jay Hannah jay at jays.net
Fri Sep 28 18:50:29 EDT 2007


On Sep 28, 2007, at 4:34 PM, Chris Fields wrote:
> On Sep 28, 2007, at 4:09 PM, Hilmar Lapp wrote:
>> and I'm wondering that there must  be a header (or at least an
>> enclosing tag) for SeqIO XML formats - so how is that dealt with
>> there?
>
> Re: (ii): I'm not sure, actually; I wouldn't be surprised if XML
> output hasn't been tested very well.

For good or ill I stole what I found in other Bio/SeqIO/* classes  
when I started writing my Bio::SeqIO::solrxml. It is not ready, but  
you can poke it with a stick here if you like:

http://vc.jays.net/viewvc.cgi/SolrGene/solrxml.pm? 
revision=26&root=CLAB&view=markup

In _initialize() it sends XML header goo into $self->_print(), and it  
uses DESTROY to drop an XML closure tag into $self->_print().

Constructing it

$out_solr  = Bio::SeqIO->new(-file => ">seq.solr.xml",
                              -format => 'solrxml');

without writing any sequences to it created a seq.solr.xml file with  
the XML header and footer and nothing in the middle.

If this is not The Right Way I'm happy to change it to do whatever.  :)

> If I could go to the Nov. GMOD meeting to help hammer out some of the
> GFF3/FeatureIO/SF::Annotated stuff I would, but I would be traveling
> on my own dime.  Maybe I'll see what I can come up with and stay at
> the no-tell motel...

I've decided to spend many of my own dimes and make the trek. I hope  
to meet many BioPerl'ers. I'll buy you dinner if you show up.  :)

Take care,

Jay Hannah
http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah





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