[Bioperl-l] Problem with StandAloneBlastPlus
dcarball at tandar.cnea.gov.ar
Mon Jul 21 15:57:42 UTC 2014
Im 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 Im passing the outfmt parameter via
-method_args => [ '-outfmt' => '"7 std qcovs"' ]
(Im using single quotes with doubles inside, so that the double quotes are
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 couldnt find the way to make it work.
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Bioperl-l