[Bioperl-l] Re: SCF File Information Lost (PR#987)

[Jason Stajich]

Mike-

Bio::SeqIO::scf is an older module.  It may not have kept up with changes to 
the Bio::Seq system.  It in fact does not have a designated maintainer as no one
has really spoken much about it recently.  Would you want to help out here?

The information you describe is specific to the sequencing procedure and as such
is probably not particularly relavent to the Bio::Seq object.  Your hack to
store the information in the desc field is a reasonable one.  Perhaps there is a
better place however as desc is read when a Sequence is written to a file by the
SeqIO system.

Perhaps someone who uses the Bio::SeqIO::scf could respond and give some advice
on how to best update the module to handle this better.

We can create a specialized instance of a Sequence -- Bio::Seq::SCFSequence or
another appropriately named object -- to handle the specialized information
needed.

Would you be able to enumerate the fields needed to capture the information that
SCF parses out which are not currently storable in the Bio::Seq objects?

Thanks,
Jason Stajich
jason@bioperl.org