[BioRuby] BioRuby's Bio::FlatFileIndex compatibility with BioPerl's Bio::DB::Flat

[Naohisa GOTO]

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