[Bioperl-l] simplealign, prediction parsers

[Richard Adams]

    Hello,
Please ignore this if it's already been fixed but there seems to be 2
problems in 1.0.2
with Bio::SimpleAlign purge function.

1.  the get_nse call produces the error
    Use of uninitialized value in numeric eq (==) at
/packages/perl/lib/site_perl/5.6.0/Bio/SimpleAlign.pm line 373, <GEN0>
line 242.
2.
    the lines
@one = $seq->seq();
   @two = $seq2->seq();
    I guess are supposed to be split so that each element is an amino
acid or - or .
    But the way the code works there will only be one element - the
whole sequence string.

I've fixed these problems for my own use so if my code would be any use
I'd gladly submit it.



I'm writing some parsers for various prediction servers, such as
Expasy's Psort, TargetP, netphos and ultimately plan to develop parsers
for some secondary
structure prediction servers.  Are people already working on this sort
of thing or would these be useful additions?

Richard

Dr Richard Adams
Molecular Medicine Centre
University of Edinburgh UK