[Bioperl-l] Issues with new Bio::Tools::Run modules for Genemark and Glimmer

Mark Johnson johnsonm at gmail.com
Wed Feb 28 14:59:09 EST 2007

    I happen to need something like Bio::Tools::Run::Genemark, so I'm coding
one up.  When I started on the tests for it, I realized I have a problem.  I
can distribute a fasta file downloaded from GenBank to use as input, but I
can't distribute the model file needed to actually run Genemark (
Genemark.hmm for prokaryotes, gmhmmp, in my case).
    It took *forever* to get a license, and I'm not thrilled with the
prospect of talking them out of a redistributable model file.  I'd love to
distribute the test, but I don't see how I'm going to be able to.
    Also, I've settled on IPC::Run instead of system().  The docs indicate
the bits of it I'm using should be OK on Windows, except maybe for Win9X.
I don't want to clutter up the console, I don't like embedding stdout/stderr
redirection in command strings, and I don't want to have to worry about
signal handling (What if the child catches a ctrl-c halfway through
parsing?  What if the parent does?).  Anybody object to that?
   One final thing.  I'm lazy, I don't want to deal with parsing arguments
to the constructor, so I'm just calling _rearrange() to deal with it.  The
Bio::Tools:: parsers all take dash options, but it looks like a bunch of the
stuff in Bio::Tools::Run:: takes dashless args.  Objections?

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