"->bits" behaviour in HMMer parsing

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"->bits" behaviour in HMMer parsing

Francisco J. Ossandón

Hello everyone,

I was checking Bio::SearchIO and found that there is an inconsistency regarding Bits value for $hit and $hsp when parsing HMMer outputs.

 

HMMer results don’t use Bits, so when Bits are requested from $hit, it returns 0 from the HMMERHit module (“sub bits { return 0 }”), but when Bits are requested from $hps, it goes to the SimilarityPair and Similarity modules and they return ‘undef’. Since $hit->bits already return 0, I think it would be consistent to also return 0 from $hsp->bits… Adding “sub bits { return 0 }” to the HMMERHSP module would do the trick.

 

What do you think?? Is it ok for me to add this to HMMERHSP and make it consistent or there could be something wrong with it??

 

Cheers,

 

Francisco

 


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