[Biopython-dev] Blast parsers and records

[Blanca Postigo Jose Miguel]

Mensaje citado por Michael Sandford <sandford at ufl.edu>:

> I've got a few comments as well:
> > 4) The current Blast record stores its information in attributes. If you
> use Bio.Entrez to parse Blast XML output (Biopython 1.54 contains the
> necessary DTDs to do so), the information is stored in dictionaries. This has
> some advantages. For example, it allows you to use record.keys() to find out
> what the record contains. Ideally, I think that a Blast Record class should
> inherit from a dictionary.

I've developed for my own use a dict structure that represents a blast result.
This structure also can represent many other results, like exonerate, SSAHA or
any other number of aligners. Having a common representations for all of them
allows you to create common filters that work with the same interface. I don't
know if it is very efficient, but it has proven to be very convinient for us.
You can take a look at:

http://github.com/JoseBlanca/franklin/blob/master/franklin/alignment_search_result.py

Best regards,

Jose Blanca

----- Fin del mensaje reenviado -----


--