[Bioperl-l] Bio::Tools::Run::StandaloneBlastPlus and outformat

Mark A. Jensen maj at fortinbras.us
Sun Feb 28 21:33:23 EST 2010

Ben -- Might be a bug; can you send your script and the error you get 
Thanks MAJ
----- Original Message ----- 
From: "Ben Bimber" <bimber at wisc.edu>
To: "bioperl-l" <bioperl-l at lists.open-bio.org>
Sent: Sunday, February 28, 2010 6:10 PM
Subject: [Bioperl-l] Bio::Tools::Run::StandaloneBlastPlus and outformat

> Not sure if this is a bug or if I'm missing something:
> In the standaloneBlastPlus wrapper, I can specify an output format
> ('-outfmt' in blastn) using '-outformat'.  blastn allows an integer to
> specify output format (ie. 6 for tabular).  It also allows a some number of
> string to specify additonal columns.  in this case, the whole block is
> quoted:
> -outfmt "6 qgi qacc sseqid sallseqid sgi sacc sallacc qstart qend sstart
> send qseq sseq length pident nident mismatch positive gapopen qframe sframe"
> The blastplus wrapper throws an error if you try to pass anything besides an
> integer as -outformat.  Is there another way to specify output format or is
> this a limitation of the module?
> thanks,
> ben
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