[Bioperl-l] BLAST to FeaturePair

L.Pollak lorenz@ist.org
Mon, 31 Jul 2000 17:51:20 +0200

Hi Hilmar, Hi Ewan!

> > 2) Bio::Tools::BPlite::HSP has several implementation short-comings from my
> > perspective: a) $feature->seqname() does not return a seq id but the full
> > BLAST description line, incl. the '>' (could be fixed easily),
> This could be done client side: Keep BPLite just "representing BLAST"
> without too much magic. But stripping '>' seems sane.

i can do that. what should be stored in $feature->seqname ?
(but as there is no full sequence object, i can't store ids and accs,
> > b) the
> > lengths of the sequences are not stored (would require additional parsing
> > code),

ok, i can parse the length, but how should i store it ?
(the feature does not contain a method for that, but i could
attach a sequence object that has correct id, acc and sequence
length but no real sequence in it...)
> > c) properties of the alignment are stored as 'new' tags, instead of
> > through the tag system. This prevents them from easy de/serialization
> > through the gff_string()/_from_gff_string() methods. (BTW does the string
> > returned by $bplite_hsp->homologySeq() make sense to anyone?)
> Talking to Lorenz - I'm not siure about this.

what properties do you mean? score, bits, P value, matching, positives 
and such things? if so then hilmar is right, they are not stored through
the tag system, but it should be no problem for me to add this!
(would both query and sbjct feature have the same tag values in this

why does the homologySeq make no sense?
(i just adopted it from the original BPlite...)

and could someone please explain to me what's the purpose of those
gff_string methods?

thank you,