[Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Nov 26 04:43:33 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2337





------- Comment #6 from ngoto at gen-info.osaka-u.ac.jp  2008-11-26 04:43 EST -------
(In reply to comment #4)
> Whoops. Naohisa didn't read the entire spec, and neither did I. He focused on
> one sentence, "There is no other data in this file", but this sentence is
> contradicted later in the spec. Check these excerpts:

Which version of spec do you have?  In obda-specs/flatfile/indexing.txt
CVS version 1.3,  I think the 5) and 7) are written only for the
"flat-file only solution" and not valid for the BerkeleyDB implementation.

The file obda-specs/flatfile/indexing_BerkeleyDB.pdf also suggests
that the file config.dat contains only one line "index\tBerkeleyDB/1\n". 

http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/obda-specs/flatfile/indexing_BerkeleyDB.pdf?rev=1.1&cvsroot=obf-common&content-type=application/pdf

In Biopython, the implementation of Bio/Mindy/BerkeleyDB.py suggests
that Biopython may also write configuration only to the  config.dat file
as text data, like BioPerl does.
http://biopython.open-bio.org/SRC/biopython/Bio/Mindy/BerkeleyDB.py

So, I think it is realistic to change the spec of the BerkeleyDB index
to follow current BioPerl's implementation (and this may be very similar 
to Biopython's implementation), because the spec has never been accurately
implemented by any major Bio* projects over 6 years.


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