[Biopython-dev] Propose: Adding an alias name (gb) for Genbank in SeqIO

[Sebastian Bassi]

As a follow up to bug 2811 where "gb" is now a valid name in
Bio.Entrez, I propose to add "gb" as an alias for "genbank" in SeqIO.
This proposal is backward compatible since previous code using
"genbank" is unaffected. The rationale behind my request is that

Entrez.efetch(db=db,id=x,rettype='gb')
When I want to save the sequence I got using rettype='gb', seems
consistent to use SeqIO.write(myseq,fielhandle,'gb')

Bugtrack chat related:

---------- Forwarded message ----------
From:  <bugzilla-daemon at portal.open-bio.org>
Date: Tue, Apr 14, 2009 at 9:13 PM
Subject: [Biopython-dev] [Bug 2811] EFetch returning ASN.1 not GenBank
format for rettype=genbank
To: biopython-dev at biopython.org


http://bugzilla.open-bio.org/show_bug.cgi?id=2811


------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk
2009-04-14 20:13 EST -------
(In reply to comment #3)
> I saw in the online Tutorial this small typo:
> "form Bio import SeqIO"

I'd fixed at least one occurange of that error before, but you are right -
there were still two left in CVS.  Thanks.

> I and have a question regarding this bug: What about adding "gb" as format
> type in  SeqIO, and mapped to "genbank". This would add consistency (if I
> retrieve a sequence using "gb" from Entrez, I expect to save it using SeqIO
> with "gb"). I think it won't hurt to have "gb" as an alias for "genbank" in
> SeqIO.

The reason we have this bug in the first place was we used an unofficial return
type in EFetch in order to use the same format name ("genbank") in both
Bio.Entrez and Bio.SeqIO - and this did make the examples straight forward.

Adding aliases (such as "gb", "gp", and maybe also "genpept" for "genbank")
might make Bio.Entrez and Bio.SeqIO a little nicer to use together after the
changes forced by this bug.  There are also several aliases used in EMBOSS that
would also make sense (e.g. "pfam" for "stockholm").  On the down side, having
more than one name risks confusion.  Bring this up on the mailing list if you
like.

Leaving this bug as fixed.

Peter


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-- 
Sebastián Bassi. Diplomado en Ciencia y Tecnología.

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