[Bioperl-l] Re: BPlite Coordinates/Strandedness w/ WUBLAST (PR#1032)

[Hilmar Lapp]

> Full_Name: Charlie Kim
> Module: BPlite
> Version: 0.7.0
> PerlVer: 5.6.1
> OS: Redhat 7.0
> Submission from: d034-dell-xps-r350.stanford.edu (171.65.17.117)
> 
> 
> BPlite doesn't seem to report coordinates of Query and Subject properly
with
> WUBLAST 2.0 reports.  It always seems to take the Start as the lower
coordinate
> and End as the higher coordinate, regardless of whether the HSP is on the
Plus
> or Minus strand.  This makes it impossible to tell which strand the Query
hits.
> 
> This could possibly be resolved by a function which reports the strand of
the
> HSP, or by reporting the actual start & end coordinates.
> 
> 

Charlie, first you should upgrade to 0.7.2, the latest stable
release. There
were indeed some bugs with the coordinate reporting in BPlite, and
these have
been fixed. Second, start for the feature objects being extracted
from the BLAST
report is by definition always lower than end. Call $hsp->strand()
to obtain
the
strand (HSP implements Bio::SeqFeatureI, and hence has all of
those methods;
since it inherits from Bio::SeqFeature::SimilarityPair, it also
has the methods
mentioned there).

        -hilmar
-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
San Diego, Ca. 92130                     phone: +1 858 812 1757
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