[Open-bio-l] flat file indexing cross check

[KATAYAMA Toshiaki]

Hi,

We are now implementing flat file indexing in BioRuby (at last:)
and want to test the index created by other Open Bio* indexer
for cross check.

How to create flat and bdb index on gbphg.seq from GenBank
and how to search the entry AB012112 in each project?
(We have BioPerl, BioPython, BioJava installed.)

Our indexer works as follows

  % bioflat --makeindex test_flat_by_bioruby --format genbank gbphg.seq
  % bioflat test_flat_by_bioruby AB012112

  % bioflat --makeindex-bdb test_bdb_by_bioruby --format genbank gbphg.seq
  % bioflat test_bdb_by_bioruby AB012112

Regards,
Toshiaki Katayama
--
Kanehisa laboratory (Bioinformatics Center)
Institute for Chemical Research, Kyoto Univ.
Gokasho, Uji, Kyoto 611-0011, Japan
TEL +81 774 38 3272, FAX +81 774 38 3269
http://web.kuicr.kyoto-u.ac.jp/~katayama/
http://bioruby.org/ (k@bioruby.org)