[Bioperl-l] Problem with StandAloneBlastPlus

Darío Carballido dcarball at tandar.cnea.gov.ar
Mon Jul 21 15:57:42 UTC 2014



I’m working with this script that uses StandAloneBlastPlus, and I would like
to take advantage of a new feature in the latest releases of blast+, which
allows me to present the query coverage in the output (among other values).
For that to work, the value of –outfmt needs to be quoted (for example,
-outfmt “7 std qcovs”), so I’m passing the outfmt parameter via


-method_args => [ '-outfmt' => '"7 std qcovs"' ]


(I’m using single quotes with doubles inside, so that the double quotes are
passed literally).


But when I run it, the quotes seem to get lost and I end up with the error I
get when I pass that value without the quotes: 


Error: Too many positional arguments (1), the offending value: std  


I have tried lots of combinations with single, double quotes, character
escaping and I couldn’t find the way to make it work.  


Any help?



Darío Carballido

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