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

Ben Bimber bimber at wisc.edu
Sun Feb 28 18:10:35 EST 2010

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

-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?


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