[Biopython-dev] Output sequence files

Sarah Kummerfeld sarah at k-k.oz.au
Thu May 24 19:11:16 EDT 2001

> Does Biopython provide anything in the field of writing out a sequence
> (Seq/MutableSeq classes in the usual GenBank/SwissProt/Fasta/... formats?

I noticed this didn't seem to be available a month or so back
and started thinking about the best place to put it. 
I didn't finish coding it because I was not sure if it should
be part of Seq/MutableSeq or in a 'writer' module. 

The first option seems best in terms of OO design and probably
usability, but it seems that most of the input in biopython
is done using a reader, so to be consistent with that it
should go in a writer module?

Also, to output meaningful genbank files I think we really need 
to operate on SeqFeature objects? In fact even fasta needs the
information in a SeqRecord object rather than just a MutableSeq?


p.s. For my own purposes I just wrote a writer module with the
formats I needed and a '# FIXME' to sort it out later :)

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