[Bioperl-l] Temporary file names in Bio::Tools::Run::StandAlonwWUBlast

[Brian Osborne]

Adam,

All tests pass with the patched code?

Thanks again,

Brian O.

> On May 26, 2015, at 4:34 AM, Adam Sjøgren <adsj at novozymes.com> wrote:
> 
>  Hi.
> 
> I just noticed a problem with the temporary file names that
> Bio::Tools::Run::StandAloneWUBlast uses.
> 
> wublast automatically tries to ungzip files that have names that match
> certain patterns - noticably files ending in "_Z".
> 
> B:T:R:StandAloneWUBlast uses B:T:R:StandAloneBlast::_setinput() to
> generate a temporary file for the query sequence.
> 
> _setinput() calls File::Temp::tempfile() without a SUFFIX (or a
> TEMPLATE), which means that when you are (un)lucky, the temporary file
> name becomes something like /tmp/i0311ckB_Z - which wublastp then tries
> to ungzip, which fails.
> 
> I have created a pull request to add TEMPLATE and SUFFIX to
> B:T:R:StandAloneBlast::_setinput()'s calls to tempfile():
> 
> * https://github.com/bioperl/bioperl-run/pull/15
> 
>  Best regards,
> 
>    Adam
> 
> -- 
>                                                          Adam Sjøgren
>                                                    adsj at novozymes.com
> 
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