[Biopython] Private '_filenames' attribute in class _SQLiteManySeqFilesDict?

Carlos Borroto carlos.borroto at gmail.com
Fri May 3 16:42:33 UTC 2013


Hi,

I'm writing a tool to index and query a local database using
SeqIO.index_db(). I want to provide something similar to:
$ blastdbcmd -db nt -info
Database: Nucleotide collection (nt)
        17,200,582 sequences; 44,123,601,625 total bases

Date: Feb 7, 2013  4:14 PM      Longest sequence: 65,476,681 bases

Volumes:
        /local/db/blast/nt.00
        /local/db/blast/nt.01
        /local/db/blast/nt.02
        /local/db/blast/nt.03
        /local/db/blast/nt.04
        /local/db/blast/nt.05
        /local/db/blast/nt.06
        /local/db/blast/nt.07
        /local/db/blast/nt.08
        /local/db/blast/nt.09
        /local/db/blast/nt.10
        /local/db/blast/nt.11
        /local/db/blast/nt.12

I have limited Object-Oriented Python's skills, actually very low
exposure to OO in general. The object returned by SeqIO.index_db() has
an attribute '_filenames' which I could use to report "volumes". I
recently read it is a common rule to mark private methods and
attributes with the starting underscore. Would it be safe to use
'_filenames' in this case? Could this attribute be converted to a
public one so it can be safely use without fear of breaking the code
in the future?

Thanks,
Carlos



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