[Bioperl-guts-l] [Bug 2707] New: 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
Wed Dec 10 10:42:12 EST 2008


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

           Summary: Bio::Tools::Run::StandAloneBlast does not quote shell
                    metacharacters in filenames, but Bio::SearchIO::blast
                    does
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: roy.chaudhuri at gmail.com


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).

I've attached an example script that demonstrates the problem.
I'd guess that B:T:R:SAB should be using Bio::Root::IO to ensure consistent
behaviour.


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