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

[Hilmar Lapp]

Peter Schattner wrote:
> 
> $report = new Bio::Tools::BPbl2seq(-file => Bio::Root::IO->catfile("t","bl2seq.out"));
> $hsp=  $report->next_feature;
> $score = $hsp->score;
> 
> which is syntax already used in BPlite.
> 
> The reason I bring this up is that scripts using BPbl2seq written since the  0.7 release (which probably worked if there was only one HSP in the bl2seq report) will now break.   I intend to display of an error message if a script uses the now-unsupported syntax.  The alternative would appear to be to redefine the old methods calls internally so they still work - but this seems like a lot of
> work to save probably a small number of scripts which will anyway work only on a limited number of bl2seq reports.
> 
> Any comments or objections to this approach?
> 

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.
When the next release series is started (the development release
series 0.9.x), there should be a note regarding this incompatibility
in the CHANGES file.

	Hilmar
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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