[BioPython] NCBIXML Blast parser Error for TBLASTN

[Peter]

Hi Alaguraj,

Welcome to the Biopython mailing list.

On Tue, Apr 8, 2008 at 8:36 PM, Sebastian Bassi <sbassi at gmail.com> wrote:
> On Tue, Apr 8, 2008 at 4:29 PM, Alaguraj Veluchamy <alaguraj.v at gmail.com> wrote:
>  > Dear people,I am stuck in parsing Blast XML output.
>
>  Give me your XML output file and your code to see the problem.
>  Maybe you can't align because the is a difference in polarity between
>  the BLAST hit and the original sequence (look at the 1 and -1 in
>  Hsp_query-frame and Hsp_hit-frame tags, does your problem happends
>  when you have 1 and -1 or even when you have both 1?).

Maybe - but I suspect the problem is you are looking at the subject
coordinates (hsp.sbjct_start and hsp.sbjct_end - these refer to the
matched sequence in the database), and not the search query
coordinates (hsp.query_start and hsp.query_end - these refer to your
input query sequence).

>  You should give us a more detailed report, including xml file and what
>  are you expecting and what are you getting.
>  If the XML file is too big, upload it to another place and tell us the
>  URL to download it.

Or better yet, if you are sure this is a bug, file it on Bugzilla.
And then attach the XML file to the bug.
http://bugzilla.open-bio.org/enter_bug.cgi?product=Biopython

Peter