[Bioperl-l] GuessSeqFormat problems

[Jason Stajich]

Albert -

I think the new guessing changes for phylip are causing havoc.   Lots  
of tests are failing t/GuessSeqFeature.t.  Can you take a look?

I was looking over this module - it seems like we probably want to  
run the tests in a particular order as some matches are ambiguous and  
we probably need to have preferred order. At least we'll know when  
something fails, what the order.

Another thing is it uses open directly instead of allowing Root::IO  
to open a filehandle.  If went to using Root::IO, it would allow  
peeking at not only a file but a filehandle/stream and then use  
_pushback after we have peeked over the first few lines, guess the  
format, then pass it along to the SeqIO/AlignIO handle appropriately.

Anyways, just thoughts...

-jason
--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/