[Bioperl-l] "->bits" behaviour in HMMer parsing

Francisco J. Ossandón fossandonc at hotmail.com
Fri Jul 25 19:00:26 UTC 2014

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??






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