[Bioperl-l] HMMER - Parse hmmpfam output using bioperl - help!!

K. Shameer shameer at ncbs.res.in
Thu May 8 08:31:22 EDT 2008


Hi Sendu,

Thanks for your quick reply. This is really useful.

Separately, One quick question, I dont have hmmer_pull.pm. I am using an
older version of Bioperl. Is there any provision to  to download and
install individual bioperl modules separately ?

Thanks,
K. Shameer




> You'll find the relevant documentation under Bio::Search::Result,
> Bio::Search::Hit and Bio::Search::HSP.
>
> Using Bio::SearchIO->new(-format => 'hmmer_pull') will also give you a
> faster parser that may behave more closely to your expectation during
> your loops.
>
> Anyway, there are various obvious-named methods you can use:
>
> $result->query_description
> $hit->score
> $hit->significance
> $hit->description
> $hit->start('query')
> $hit->end('query')
> $hsp->start('query')
> $hsp->evalue
>
> etc.
>




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