[Biopython] how to get the hit length from Bio.Blast.NCBIXML?

[Peter Cock]

On Sun, Mar 7, 2010 at 2:55 PM, Ann Loraine <aloraine at gmail.com> wrote:
> Hello,
>
> I'm using Bio.Blast.NCBIXML to parse blastx results for an annotation
> project. I'm searching contig consensus sequences (assembled from 454
> reads) against a protein database.
>
> Since these are assembled ESTs and may be incomplete, I need to know
> how much of a matched sequence was included in the alignment so that I
> can compute the percent coverage of both the hit and query.
>
> How do I retrieve the "hit length" from the objects returned by the parser?
>
> I couldn't find anything in the record and alignment objects that
> contains this information -- if it is not there, should it be added?

Hi Ann,

I think you are looking for the BLAST alignment's length attribute, or
perhaps the HSP's align_length attribute.

Peter