[Bioperl-l] Bio::Tools::HMMER

Mick Watson michaelwatson@paradigm-therapeutics.co.uk
Fri, 21 Jun 2002 14:05:36 +0100


I've noticed that:


returns a lits of Set objects in no particular order - would be nice if
these were returned in the order they were encountered in the hmmsearch
output file!

The following are some possible fixes.

Instead of using:

    return @array:

To sort by bit score ascending or descending:

    return sort {$a->bits <=> $b->bits} @array;
    return sort {$b->bits <=> $a->bits} @array;

To sort by evalue ascening or descending:

    return sort {$a->evalue <=> $b->evalue} @array;
    return sort {$b->evalue <=> $a->evalue} @array;

I realise that this can all be done by the user subsequent to getting
the Set objects returned as an array, however, surely there should be
some consistency - the Bioperl BLAST objects return hits in the order
they appear in the blast output, so HMMER::Results should also return
the hits in the same order as in the hmm output file.... shouldn't it?