[Biopython-dev] Output sequence files

[Iddo Friedberg]

Hi all,

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

I see that FastaAlign does that, but I cannot find anything for a single
sequence.

If Biopython really does not provide this feature, maybe a discussion
could be started. Writing out the sequence part is easy. Can be
implemented with a few functions (to_fasta, to_swiss), or those can even
be methods within Seq/MutableSeq

Why?

Well, basically there is a need for some sort of interface with the common
run-of-the mill sequence handling packages which lack APIs such as the
Wisconsin package, Clustal, etc.  (OK, maybe not Clustal, FastaAlign took
care of that, but you get my drift).

Currently, using files is the best approach, and would provide a practical
solution for people who work with these packages, but which  use
Biopython as well.

Annotation, as usual, is the problem. (SeqRecord in Biopythonese).

There was some discussion a couple of days ago regarding uniform
vocabularies. From what I gathered from the discussion, this is at a
pretty preliminary stage. My personal feelings are that this should not be
an obstacle to providing some practical tool for writing a skeleton
annotation containing, say, accession numbers, organism, keywords and
refs. This can always be expanded/modified later when some standardization
scheme comes in.

OK, I think I should stop here. I hope I'm not raising some sort of moot
point. If I'm not way off the mark, I can provide a couple of more
specifics. If I am, please chalk this up to me being out of the loop for a
while, and not reading the archives carefully.

Iddo

--

Iddo Friedberg                                  | Tel: +972-2-6758647
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/