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

[Fields, Christopher J]

This might argue for setting up bioperl-run on travis-ci :)

chris

> On May 27, 2015, at 11:24 AM, Brian Osborne <briano at bioteam.net> wrote:
> 
> 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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> 
> 
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