[Bioperl-l] SeqIO cleanup

[Jason Stajich]

I'm starting to do some stringent Bio::SeqIO cleanup (working towards
diffless round tripping that Kris Boulez suggest a while ago and Elia and
I agree is the right thing to do here).

Couple of things I've noticed - some SeqIO implementations won't accept a
PrimarySeq to write_seq.  This is probably bad...  How should a module
like embl proceed if it gets a PrimarySeq in write_seq - currently it
balks.

Also, some routines return a Seq object always rather than what fasta does
with next_primary_seq and next_seq - should this be the same behavior
everywhere?

I'll have my inplace diffing script committed soon - it does depend on
String::DiffLine to do cross-platform diffs, I can write it as a script or
even make it into a t/t test if String::DiffLine is installed on the
system.  Does that sound like a good idea - otherwise it can just be a
script in scripts/ or examples/ or a new dir utilties? (can never decide
where to put things).

-jason


Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/