[Biopython-dev] New Bio.SeqIO code

[Chris Lasher]

Just pitching in again, I agree with Michiel with regards to the list
of functions necessary. To restate, these would be:

(*) 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

I also think there's wisdom to Michiel's statement it's easier to add
functionality than it is to remove it.

I agree with Iddo on his arguments against dealing with filename
extensions. Upon reflection, however, I feel comfortable with a
lookahead-based file-format guesser for the sake of convenience and as
a matter of compromise to those who are not keen on being explicit in
regards to every detail. It's been stated that bio file formats are
quite distinct. I tried to think of a counterexample but failed.

Finally, to reply to Michiel's question on release, it does seem once
SeqIO is solidified this would certainly be worthy of a new release.
SeqIO is a big step in a good direction for BioPython.

Chris