Re: Temporary file names in Bio::Tools::Run::StandAlonwWUBlast
Mark A Jensen <[email protected]>
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Nooooooooo....... On Wed, May 27, 2015 at 2:36 PM, Fields, Christopher J < [email protected] [[email protected]] > wrote: This might argue for setting up bioperl-run on travis-ci :) chris > On May 27, 2015, at 11:24 AM, Brian Osborne <[email protected]> wrote: > > Adam, > > All tests pass with the patched code? > > Thanks again, > > Brian O. > >> On May 26, 2015, at 4:34 AM, Adam Sjøgren <[email protected]> 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 >> [email protected] >> >> _______________________________________________ >> Bioperl-l mailing list >> [email protected] >> http://mailman.open-bio.org/mailman/listinfo/bioperl-l > > > _______________________________________________ > Bioperl-l mailing list > [email protected] > http://mailman.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/bioperl-l _______________________________________________ Bioperl-l mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/bioperl-l