[Bioperl-l] SeqIO fixing: detecting if a filehandle is open for
Peter van Heusden
pvh at egenetics.com
Thu Aug 5 10:13:38 EDT 2004
Hilmar Lapp wrote:
> Quite frankly IMNSHO if you open a file for reading and then -
> unsuccessfully - try to write to the file this is not a bioperl error,
> or perl error for that matter, but a programming error. Perl will be
> no more verbose if you do this ... at least as far as I'm aware.
> I.e., the documentation should be that if you do an operation to a
> file or SeqIO handle for which you did not open it in the first place
> then the behavior is undefined.
Yep, as I said in my documentation, the options are fix the
documentation or fix the code. I acknowledge that this is programming
error - but the implication is that a single typo (no '>' when opening
the file) results in silent failure - i.e. it appears to work, but
doesn't. The Perl behaviour is slightly different (not that I think
anyone checks these things): if you do 'print $fh "FOO\n"' and $fh is
open for reading only, the return value of print is undef (otherwise it
There might not be anything do-able about this case, but as far as
possible I think that reasonable programmer errors should be caught.
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