[Bioperl-l] standalone blast outformat

[Jason Stajich]

Assuming 1 HSP you can do:

my $qcov = $hsp->query->length / $query->length;

Otherwise you have to add up the HSPs and their coverage (and remove redundancy of overlapping hits) to determine what parts of the query were aligned across all the HSPs that were found. You can try the tile_hsps function to also get this. Or if you are using WUBLAST you can get the -links option to grab the logical groups of non-overlapping HSPs to tile across.

Or use FASTA or SSEARCH which will provide a single longest path through the alignment.


On Oct 29, 2013, at 10:12 PM, Florent Angly <florent.angly at gmail.com> wrote:

> Hi Dimitar,
> 
> I suppose you are using BLAST+, not legacy BLAST. There is a HOWTO
> here that can get you started:
> http://www.bioperl.org/wiki/HOWTO:BlastPlus
> 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.
> Best,
> 
> Florent
> 
> 
> 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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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org