[Bioperl-l] internal code review of Bio::Search
Tue, 5 Feb 2002 12:37:52 -0500 (EST)
When people are interested in what fraction of a HSP is identical
or conserved - one is typically looking for the fraction identical in the
HSP or relative to the whole sequence?
I assume relative to just the portion that is participating the HSP, but
just wanted to make sure... Does anyone else have code that calculates
this so I can validate my implementation - I have been doing
it against the entire length of the hit/query not the smaller portion
in the HSP which I believe is wrong and am currently fixing that.
In the Bio::Search::HSP objects I think there are some confusing parts wrt
to length - any help in nomeclature or docs would be appreciated.
(part of Hilmar's original SimilarityPair/FeaturePair which I have kept
$hsp->query->seqlength - length of the entire query piece
$hsp->query->length - length of the query participating in the HSP
"" ditto s/query/hit/
(my added method to get at the HSP length)
$hsp->hsp_length - length of the HSP (which includes gaps added
from query and hit)
(Steve's HSPI length methods - see Bio::Search::HSP::HSPI for docs)
$hsp->length('total') - length of the HSP
$hsp->length('query') - length of the query in the HSP
$hsp->length('hit') - length of the hit in the HSP