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

[Mark A Jensen]

Nooooooooo.......

On Wed, May 27, 2015 at 2:36 PM, Fields, Christopher J < cjfields at illinois.edu [cjfields at illinois.edu] > wrote:
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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/bioperl-l
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l


_______________________________________________
Bioperl-l mailing list
Bioperl-l at mailman.open-bio.org
http://mailman.open-bio.org/mailman/listinfo/bioperl-l
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/bioperl-l/attachments/20150527/dcda47bf/attachment.html>