[Bioperl-l] Bio::Tools::BPbl2seq

[peter schattner]

Hilmar Lapp wrote:

> I don't think you necessarily have to keep supporting the old syntax
> if you don't want to. However, it has to continue to work on the 0.7.x
> branch, so you probably will want to leave it unchanged on the branch.

I've committed changes to BPbl2seq.pm (and supporting modules) to the main trunk of the bioperl-live enabling BPbl2seq to read all HSPs in a bl2seq report.  The calling syntax has necessarily changed a little and is documented in BPbl2seq.pm.  Examples of usage can be found in upated BPbl2seq.t and bptutorial.pl.

As suggested, I have not changed any code in the 0.7.x branch.  Consequently to read multiple HSPs with BPbl2seq it is currently necessary to checkout the bioperl-live main trunk.  I have tested the code and it appears to be working fine;  however, I would be appreciative if those of you who having been using BPbl2seq (or who have wanted to use it, if it could read multiple HSPs) would try it
out and let me know if any further bugs remain lurking within. (Note: this should resolve Bioperl Bug #940.)

Peter