[Bioperl-l] RepeatMask Files Saving

[Shawn Hoon]

What you could do is use the save_tempfile option which will prevent 
the files from being deleted.

$fact->save_tempfiles(1);
my @feats = $fact->mask($seq);

print "Files are saved at ".$fact->tempdir

although they will have some weird system. There is limited support for 
the wrappers
in specifying the output file names currently.

> 	Or, i suppose, a way to import repeat maker results into the
> RepeatMaker module from a repeatmasker file


You will want to use the parser which is in Bio::Tools::RepeatMasker in 
the core bioperl-live package.


shawn

> .  I didn't see anything in the
> RepeatMask.pm but I know that it uses temporary files through 
> wrapperbase.
> Is there a way to tell wrapperbase to use a file instead of running the
> program and also to save the files after a run?
>
> thnx Keith Boroevich
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