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Old 12-02-2014, 01:25 PM   #4
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
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At the command line,
Code:
$ blastn -help
...
You are looking for the -outfmt option, which can be simply a number, say 6 for tabular, or a quoted string like "6 std stitlesall" where you list the fields you want (std is shorthand for the default 12 columns).

You can do this via the BLAST+ wrapper object in Biopython too, but be careful about the quotes - see https://www.biostars.org/p/95911/
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