[Biopython] filtering by query coverage

[Peter Cock]

Hi Pathmanaban,

No, I meant instead of using the BLAST XML output, you could
run BLAST requesting tabular output.

If you want to use the BLAST XML output, I think you will need
to loop over each hit's HSPs and calculate the query coverage
(since I don't think this information is provided precalculated)

Regards,

Peter

P.S. Please CC the mailing list in your reply.

On Mon, Mar 31, 2014 at 3:44 PM, Pathmanaban Ramasamy
<rpathmanaban1 at gmail.com> wrote:
> Hi Peter ,
>     Thanks for your mail. Yes query coverage i mean by the regions with hits
> (no gaps). So u say that i can blast using standalone blast version and then
> parse them as usual xml parse in biopython?
>
>
> On Mon, Mar 31, 2014 at 3:33 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> 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
>
>
>
>
> --
> Pathmanaban