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

[Adam Sjøgren]

  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