[Bioperl-l] Bio::FeatureIO::gff bug?
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 Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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