[BioRuby] More Bl2seq questions

[GOTO Naohisa]

Hi,

On Thu, 08 Sep 2005 17:05:13 -0500
Trevor Wennblom <trevor at corevx.com> wrote:

> Another question regarding Bl2seq.
> 
> This works:
>   Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, filename_bl2seq_output) 
> do |ff|
>     ff.each do |rep|
>       rep.iterations.each do |itr|
>         itr.hits.each do |hit|
>           a = hit.identity
>         end
>       end
>     end
>   end
> 
> But this doesn't:
>   Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, filename_bl2seq_output) 
> do |ff|
>     ff.each do |rep|
>       rep.iterations.each do |itr|
>         itr.hits.each do |hit|
>           a = hit.percent_identity
>         end
>       end
>     end
>   end
>
> To make it work I have to go down to the HSP level: 
>   Bio::FlatFile.open(Bio::Blast::Bl2seq::Report, filename_bl2seq_output) 
> do |ff|
>     ff.each do |rep|
>       rep.iterations.each do |itr|
>         itr.hits.each do |hit|
>           hit.hsps.each do |hsp|
>             a = hsp.percent_identity
>           end
>         end
>       end
>     end
>   end
> 
> 
> Shouldn't we be able to see percent_identity, percent_positive, 
> positive, etc. on the hit level?

This is because bl2seq (and BLAST) reports percent_identity on every
Hsp and does not report percent_identity for Hit. Hit#identity is only
a shortcut method of hsps[0].identity. It is prepared because of keeping
compatibility(polymorphism) with Fasta::Hit class which doesn't have Hsp.
percent_identity is not prepared for Hit object because Fasta::Hit does
not have it. Please use hsps[0].percent_identity instead. Note that
percent identity of each Hsp means identity / alignment length of Hsp
and cannot always be applyed to hit.

-- 
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Department of Genome Informatics, Genome Information Research Center,
Research Institute for Microbial Diseases, Osaka University, Japan