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

Chris Fields cjfields at uiuc.edu
Sat Sep 29 14:28:16 EDT 2007


On Sep 28, 2007, at 5:50 PM, Jay Hannah wrote:

> 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 you do it this way you should probably run a check on the mode()  
the object state is in ('r'=read, 'w'=write, '?'=unknown), and only  
_print() on write mode.  Might also be a good idea to implement a  
next_seq with an exception ('Module is write only').

>> 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

I may see what I can scrape up myself but it doesn't look good (lab's  
closing down soon, so money's pretty tight).  If I knew about the  
meeting a while in advance I would probably have made it.  Oh well!

chris



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