[Bioperl-l] standalone blast outformat

dimitark at bii.a-star.edu.sg dimitark at bii.a-star.edu.sg
Wed Oct 30 03:45:29 UTC 2013

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


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