[Bioperl-l] StandAloneBlast : 2 newbie questions

[Peter Schattner]

Alexandre Irrthum wrote:

> Two naive questions about the StandAloneBlast module.
>
> In the following script, the call to blastall doesn't seem to work
> because I modify the input record separator variable $/.

I believe that $/ is a global variable in perl and consequently I would
not be surprised that changing its value might well confuse any bioperl
modules that input and parse data (such as BPlite.pm or Blast.pm, and,
implicitly, StandAloneBlast.pm) .  To accomplish what I think you are
trying to do I would set $/ = ".." in your script immediately before your
input statement where you want the atypical record separator, and I would
return it to its default value, $/ = "\n"  as soon as you are finished
and definitely before you start calling bioperl modules that do their own
I-O.  Hopefully that should help.

>
> I have to perform a large number a blast iterations and would like
> to avoid accumulation of temporary input sequence files in /tmp.
> Can I get the name of these files after each iteration to unlink them,
> or is there another way ?

Interesting question that I don't have a good answer to.  Can you help on
this, Jason?

- Peter