[Bioperl-l] Bio::SeqFeature::SimilarityPair->from_searchResult()?

John SJ Anderson genehack at genehack.org
Thu Aug 12 20:32:07 EDT 2010


On Aug 10, 2010, at 21:54 , Douglas Hoen wrote:

> I was wondering why the Synopsis in the docs for Bio::SeqFeature::SimilarityPair has the following:
> $sim_pair = Bio::SeqFeature::SimilarityPair->from_searchResult($blastHit);
> 
> There doesn't actually seem to be a from_searchResult method. Am I missing something?

No, it looks like that method got removed back in 2002 as a part of moving to Bio::SearchIO (which was removed still later...):

  <http://github.com/bioperl/bioperl-live/commit/5e3bdc11eb0ceffcd8e8966299a6367e792f2fd1>

Unfortunately, the commit didn't update the documentation. From the tiny little bit I've looked at the code, it looks like you should just be calling the 'new()' method instead (note that it takes a set of arguments, not just a BLAST hit object).

Hope this helps -- if you should happen to have the tuits, a patch to update the documentation to reflect the current interface would be awesome...

chrs,
john.




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