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

Sendu Bala bix at sendu.me.uk
Thu May 8 08:57:34 EDT 2008


K. Shameer wrote:
> Dear All,
> 
> Here is the code snippet I used to get the hit name and hit length from an
> hmmpfam file. I need to add the sequence start and end information
> (query), description of domain, score and e-value.
> 
> I checked for the available method in deobfuscator, but I couldn't find
> the details i wanted. Is there methods available in the Bio::SearchIO or
> related modules.
> __CODE__
> $input = shift;
> use Bio::SearchIO;
>     my $in = Bio::SearchIO->new(-format => 'hmmer',
>                                -file   => $input);
>     while( my $result = $in->next_result ) {
>         while( my $hit = $result->next_hit ) {
>             print $hit->name(),"\t";
>             while( my $hsp = $hit->next_hsp ) {
>                 print $hsp->length(), "\n";
>             }
>         }
>     }

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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