Hi all ...

I'm using Biopython 3.4.1 with Blast 2.2.29 and I'm trying to get the query coverage of some blast search beside the default report info in tabular format using `-outfmt 6` as following :

    comline=NcbiblastxCommandline(cmd='blastn',query="A.fasta",db="B.db",evalue=0.001,outfmt='6 qcovs',out="result.txt")

But it throws the following error:

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

I know it seems a very basic question ,but it's seriously driving me crazy ,since I spent two days trying to figure out the solution for this error and nothing seems to fix it !!

Some threads have addressed this issue and suggested to rewrite the command by hand instead of copying and pasting ... I did rewrite it by hand like thousand times and the error pertains .

Also, I have tried to run it from the Command Prompt cmd and again it threw the same error!!

Is there anyway to get around this problem?

Many thanks in advance
Did you try `outfmt='"6 qcovs"'`? The command string needs to literally contain these quotes, such that the command line looks like:

    blastn -outfmt "6 qcovs" ...