[BioPython] NCBIStandalone Parser problem
edeveaud at pasteur.fr
edeveaud at pasteur.fr
Tue May 17 05:57:28 EDT 2005
On Tue, Apr 26, 2005 at 05:25:59PM +0900, Michiel Jan Laurens de Hoon wrote:
> Could you try this again with Biopython version 1.40b and see if the
> problem still occurs there? If so, could you send me the query that you are
> using so I can replicate this error?
sorry for the long delay, but know as course finished I will have more time
to dig into the problem.
anyway I reproduced the same error with Biopython version 1.40b
if you want to check with the datas I provided a tar.gz of all the necessary
files here
<URL:http://instcard1.free.fr/biopython_test.tgz>
the tarball contains :
*) a bank containing the following 2 sequences CV793585 and
CV793586 taken from the genbank nc0421.flat update
*) the generated index for this one (formatdb -p F -i test_bank)
NB this ones may need to be rebuild
*) 2 query files
query_ok: a query giving some hits
query_crash: the query that does produce '***** No hits found ******'
and leads the parser to crahs
*) the basic python script used
python ./crash.py query_ok bank/test_bank
python ./crash.py query_crash bank/test_bank
Eric
--
E> desole mais je n est pas trop l habitude des groupes de discutions
Leçon n° 1 : on répond en haut et on vire le message auquel on répond
Cette suppression facilite grandement la lecture !!!
-+- DrN in <http://neuneu.mine.nu> : Le Neuneu par l'exemple -+-
More information about the BioPython
mailing list