[Bioperl-guts-l] [Bug 2707] Bio::Tools::Run::StandAloneBlast does not quote shell metacharacters in filenames, but Bio::SearchIO::blast does

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Dec 11 00:05:26 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2707


cjfields at bioperl.org changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #2 from cjfields at bioperl.org  2008-12-11 00:05 EST -------
(In reply to comment #0)
> I'm having a problem using Bio::Tools::Run::StandAloneBlast with a filename
> that contains shell metacharacters. It looks like
> Bio::Tools::Run::StandAloneBlast does not quote metacharacters but
> Bio::SearchIO::blast does. This means that if I have an awkward filename like:
>  $filename='needs(quoting)';
> then B:T:R:SAB throws an exception "blastall call crashed", since blastall
> crashes when it can't write an output file with that name. However, if I quote
> the name:
>  $filename=qq('needs(quoting)');
> then B:T:R:SAB is perfectly happy, but when I try to read the results file
> Bio::SearchIO::blast throws an exception (via Bio::Root::IO) since it can't
> find a file called 'needs(quoting)' (including the quotes).

Roy, I committed a fix which quotemeta's file names temporarily in
StandAloneBlast while building the parameter strings.  Seems to handle both
your cases as well as other odd ones like 'needs"quoting"'.

Thanks!


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