[Biopython] filtering by query coverage

Peter Cock p.j.a.cock at googlemail.com
Mon Mar 31 13:33:26 UTC 2014


On Mon, Mar 31, 2014 at 2:28 PM, Pathmanaban Ramasamy
<rpathmanaban1 at gmail.com> wrote:
> Hi i am new to biopython and i would like to filter my xml outfile based on
> Query coverage percentage. Can someone help me with this? thanks in advance

How are you defining query coverage percentage?

It might be simpler to use BLAST+ 2.2.28 or later with the tabular output
and specifically include one of these columns:

            qcovs means Query Coverage Per Subject
          qcovhsp means Query Coverage Per HSP

Filtering tabular BLAST output on query coverage would then be easy.

Peter



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