[BioRuby] BioRuby's Bio::FlatFileIndex compatibility with BioPerl's Bio::DB::Flat
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Sun Jul 22 10:48:42 UTC 2007
On Sun, 22 Jul 2007 19:25:00 +0900
Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp> wrote:
> In addition, I also tried flat database.
>
> % bp_bioflat_index.pl --create --format fasta \
> --location /tmp/flat --dbname testflat --indextype flat \
> /tmp/flat/tmp.fst
>
> % cat testflat2/key_ACC.key
This is my typo. I meant
% cat /tmp/flat/testflat/key_ACC.key
> 19TEST00001 0 0 100 TEST00002 0 100 100TEST00003 0 200 100TEST00004 0 300 50
>
> It sesms that the index is correctly created.
The index was not correct.
The size of TEST00004 is misrecognized as 50 (should be 100).
I think this is also a bug in BioPerl.
Regards,
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ngoto at bioruby.org
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