[Bioperl-l] Clean-up of Bio::Root::IO

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Wed Oct 4 05:21:24 UTC 2006

Hi all,

Now that we have Perl 5.6.1 as a minimum, the following modules are 
standard: File::Spec, File::Temp, File::Path

Bio::Root::IO has functions catfile(), tmpdir(), tmpfile(), rmtree() 
which currently dispatch to the File:: version, or try to emulate it. We 
don't need to emulate anymore. Jason Stajich suggested in a previous 
post that they should be deprecated, and that users should use directly 
the File:: functions themselves.

I have an uncommitted simplified version of Bio::Root::IO which does 
this, and "all tests pass". The functions currently (silently) dispatch 
directly to their native counterparts.

The only tricky function is tempfile() which is *mostly* like 
File::Temp::tempfile(), but does some voodoo of converting 
(TEMPLATE=>'xxx') to the non-hash first parameter of the File:: version, 
so I'm hesitant to commit. It may do other magic - Hilmar?


Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia

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