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

Hilmar Lapp hlapp at gmx.net
Fri Sep 28 17:09:28 EDT 2007


On Sep 28, 2007, at 12:04 PM, Chris Fields wrote:

> In general I don't think SeqIO classes generates actual output  
> (like the GFF header information) in the constructor

There's probably two reasons they don't (if really all of them  
don't): i) unless you explicitly test (how?) whether the file has  
been opened for writing, you actually don't know in the SeqIO  
constructor whether someone's going to write to the file or read from  
it. ii) off hand, I don't know of a sequence file format that would  
require a particular header being written just once.

Though thinking about this, I start asking myself whether i) wouldn't  
also apply to FeatureIO (are we not reading gff too in this class?),  
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?

	-hilmar
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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