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Does Ncbitblastncommandline Reads The Outfmt (Options 6, 7, And 10 ) Correctly?

I am trying to call 

tblastn_hits = NcbitblastnCommandline(cmd='tblastn',
                                         query=query_handle,
                                         db=db_handle,
                                         num_threads=6,
                                         evalue=0.001,
                                         outfmt="6 qstart qend evalue bitscore",
                                         dbsize=10000000,
                                         out="%s%s.txt" % (result_handle,orf_name))

But, when i run the script, it ignores anything after 6 in outfmt, so the blast results only have default columns. Is this a problem with the Biopython version or i am doing something wrong?

biopython blast blast
• 5,267 views • link
updated by Ram Ram • written by microbeatic microbeatic

I'm having the same issue when running blast+ executables straight from command line.

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written by gammyknee gammyknee

1 answer

You need to quote it, the easiest way would be:

tblastn_hits = NcbitblastnCommandline(cmd='tblastn',
                                     query=query_handle,
                                     db=db_handle,
                                     num_threads=6,
                                     evalue=0.001,
                                     outfmt='"6 qstart qend evalue bitscore"',
                                     dbsize=10000000,
                                     out="%s%s.txt" % (result_handle,orf_name))

Here I am using single quotes for the Python string, which means I can use double quotes inside the string.

• 134 views • link
updated by Ram Ram • written by Peter Peter

Yes, thank you! I was having this problem on blast+ on the command line when combining it with GNU Parallel.

• 0 views • link
written by johnsenkyle13 • johnsenkyle13

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