[Biopython-dev] New Bio.SeqIO code

[Michiel de Hoon]

Peter (BioPython Dev) wrote:
> Currently the individual format specific iterators just require a handle
> (and not a filename).  Are we all happy with this?

Happy.

> We could make the handle and format the first arguments as a compromise?

If in doubt, don't add it to Biopython!
It's much easier to add a functionality later, should the need arise, 
than to remove one.

> I personally want the file extension to format mapping, but then I am
> fairly disciplined about using file extensions.  As I seem to be the
> only voice advocating this, it looks like I may have to give in...
> 
> Is it worth asking on the main discussion list to canvas opinion?

Sure, go ahead. But ask for *why* a user wants file extension to format 
mapping (so just "Yeah, I'd like that..." doesn't count). I'd like to 
know which usage case that we haven't thought about yet warrants file 
extension to format mapping.

> We have functions to do the following, where "file" may mean just a
> handle, or perhaps the choice of a handle or filename (see above):
> 
> (*) File to SeqRecord iterator, currently File2SequenceIterator
> (*) SeqRecord iterator/list to dictionary, currently SequenceIter2Dict
> (*) SeqRecord iterator/list to alignment, currently Iter2Alignment
> (*) Write SeqRecordwher iterator/list to a file, currently Sequences2File

If:
   File2SequenceIterator doesn't infer the file format from the extension
and
   File2SequenceIterator takes handles only, so no file names,
then:
   Why do we need the File2SequenceIterator function?

Btw, we should make a new Biopython release once the dust settles.

--Michiel.