[Bioperl-l] Empty FASTA files with Bio::SeqIO

Hilmar Lapp lapp@gnf.org
Tue, 19 Dec 2000 15:41:28 -0800

"J.C. Diggans" wrote:
> I'm fairly sure this has come up in months past but a quick search of
> the archives turned up nothing. Bio::SeqIO chokes when trying to read in
> files that have one or more empty FASTA sequences. Was this
> functionality desired or just a by-product of the parsing method? Empty
> sequences are all too possible in a production environment so was this
> decision intentional or would a patch be useful?

It indeed came up some months ago, and it should be somewhere in the
archives. The current design is intentional, but we decided to support
empty sequences and reading and writing them in FASTA format (NOT in other
formats). This will be part of the 0.7 release features. If you look at the
task list, you'll find it.


Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757