[Bioperl-l] HMMER

[Ewan Birney]

On Thu, 10 Oct 2002, Vilanova,David,LAUSANNE,NRC/BS wrote:

> Hello,
> I have modified domain.pm and results.pm to retrieve the HMM model
> description by adding a hmmdesc method.
> This method will parse out the Hmm model description.
> 
> For exemple when parsing hmmpfam you can use it like this:
> foreach $seq ( $res->each_Set ) 
> 		{
> 					
> 				foreach $domain ( $seq->each_Domain ) 
> 				{
> 					print " Hmm domain
> ",$domain->hmmname," Description ",$domain->hmmdesc,"\n";
> 				}
> 		}
> 
> The output will be:
> Hmm domain AFP Description Insect antifreeze protein
> 
> Shall I post the files or can I have an account in the cvs repository.
> By the way the method write_ascii_out seems to be buggy. Is anybody working
> on that ???


Please post the file to me David.



I think the aim is to move all of this to the SearchIO system - have you 
looked into using the SearchIO system which does have a HMMer parser?


Bio::Tools::HMMer will remain for one or two more releases for backward 
compatibility






> 
> David
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> 

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