[Biopython-dev] NCBI-XML blast parser

[david coornaert]

Peter wrote:
> Hi David
>
> Could you file a bug and attach your patch to it please?  (Trying to 
> send attachments to the mailing list can be a bit unreliable).  Then 
> hopefully some of the group can at least try it out...
>
>   
Well I'm not sure about bug procedure
so here's it already
I'll have a look at the list stuff quite soon and will submit as requested

I wouldn't have qualified that as a bug, just wondering why would
someone consider
this values as useless, sure you can calculate these, altho it would be
painfull and ... well since it
is already in the XML...
I simply added these (in red) :

Bio/Blast/NCBIXML.py

line 289:
# No need for Hsp_query_to
def _end_Hsp_query_to(self):
"""offset of query at the end of the alignment (one-offset)
"""
self._hsp.query_to = int(self._value)

def _end_Hsp_hit_from(self):
"""offset of the database at the start of the alignment (one-offset)
"""
self._hsp.sbjct_start = int(self._value)
# No need for Hsp_hit_to
def _end_Hsp_hit_to(self):
"""offset of the database at the end of the alignment (one-offset)
"""
self._hsp.sbjct_to = int(self._value)



Conversely, a real bug is the mess that is occuring regarding Frame and
Strand !!

in a blastn output must appear:

Strand = Plus / Plus
or
Strand = Plus / Minus (and so on)

while in a tblastx must appear:
Frame = +3/-1 (and so on)

blastx (must also present one Frame info)

unfortunately to find the appropriate strand in a blastn job, you need
to address
the hsp.frame array , eventho there's a hsp.strand array...


And all this stuff is usefull !! if it is the opposite strand you need
to swap query_start and query_to for example...



> Out of interest, what version of Blast have you been using?  Online or 
> standalone?
>
>   
well I've seen the complains regarding 2.2.14 , Hence I sticked to
2.2.13 standalone

=;B^)


-- 
===============================================
David Coornaert [PhD]   (dcoorna at dbm.ulb.ac.be)

Belgian Embnet Node (http://www.be.embnet.org)
Universite' Libre de Bruxelles

Laboratoire de Bioinformatique
12, Rue des Professeurs Jeener & Brachet
6041  Gosselies
BELGIQUE

Te'l:  +3226509975
Fax:  +3226509998
===============================================