[Bioperl-l] standalone blast outformat

Florent Angly florent.angly at gmail.com
Wed Oct 30 05:12:43 UTC 2013

Hi Dimitar,

I suppose you are using BLAST+, not legacy BLAST. There is a HOWTO
here that can get you started:
Regarding your issue, I had a look at the blastn manual, and I doesn't
look like you can write '-outfmt "7 qcovs ..."' to me. If anything, it
would be '-outfmt "qcovs ..."'.
So, maybe try to get your command to work as intended in a terminal
before putting it in BioPerl.


On Wed, Oct 30, 2013 at 1:45 PM,  <dimitark at bii.a-star.edu.sg> wrote:
> Hi guys,
> i was wondering how can i get the query coverage when blasting with Bioperl.
> So i figure out one way is to specify the outformat to tabular(7) and the
> specify that i want the qcovs(query coverage per subject). From BLAST manual
> i see one can do: -outfmt "7 qcovs ..." but in Bioperl i can only say:
> -outformat => 7. If i do: outformat => "7 qcovs" i get an error.
> Well another option i suppose is to get the lengths of all hsps from a hit
> and estimate the query coverage that way but im not exactly sure if this is
> correct way.
> Any idea how can i get the query coverage?
> Thank you very much for your time and any hints
> Regards
> Dimitar
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