[BioPython] Why _num_letters_in_database XMLBLAST parser?
Michiel de Hoon
mjldehoon at yahoo.com
Mon Mar 31 11:54:39 UTC 2008
Also see bug report 2176 for other naming inconsistencies between the different Blast parsers.
http://bugzilla.open-bio.org/show_bug.cgi?id=2176
Peter <biopython at maubp.freeserve.co.uk> wrote: On Mon, Mar 31, 2008 at 2:28 AM, Sebastian Bassi wrote:
> Hello,
>
> I am working at the xml formater (to format BLAST xml to html).
> I found that the num_letters_in_database data is stored as a "private"
> attribute.
>
> When I want to retrieve the num_letters_in_database I have to do:
>
> >>> fr=NCBIXML.parse(open(f_in)).next()
> >>> fr._num_letters_in_database # SEE THE _ before num_letter_in_database
> 4662239
That looks like a bug to me. The old text parser in
Bio.Blast.NCBIStandalone and the Bio.Blast.Record both use
num_letters_in_database with no leading underscore.
If there are no objections, I'm happy to make that change.
Peter
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