[Bioperl-l] BLAST to FeaturePair

hilmar.lapp@pharma.Novartis.com hilmar.lapp@pharma.Novartis.com
Mon, 31 Jul 2000 13:40:58 +0100

Dear all,

we need to convert BLAST hits into FeaturePair objects. As I've noticed
this is already realized by Bio::Tools::BPlite::HSP.

However, I have some problems with this.
1) I need the HSP tiling functionality of Blast.pm, which may be beyond the
scope of a lightweight BLAST parser like BPlite. Likewise, I need the
statistics about the alignment as neatly gathered by Blast.pm.
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), b) the
lengths of the sequences are not stored (would require additional parsing
code), 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?)

What do you think of having the ability to turn a Bio::Tools::Blast::Sbjct
object into a FeaturePair, too. Possibilities for implementation could be
to make Sbjct.pm inherit off FeaturePair, or to add a method as_featurePair
() which returns what it suggests. I favor the latter.

Feedback appreciated.