Temporary file names in Bio::Tools::Run::StandAlonwWUBlast
[email protected] (Adam Sjøgren)
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Organization | Novozymes A/S (reg. no.: 10007127) |
| Message-ID | <[email protected]> |
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]
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