> Would this not keep requesting/submitting additional (duplicate) BLAST
> queries?
>>
>> try:
>> this_result = get_BLAST(id)
>> result_dict[id] = True
>
I assumed that
NCBIWWW.qblast
waits for a response from the server.
Are you saying that instead it queues a request, a
On Wed, Dec 25, 2013 at 11:24 PM, Jason Friedman wrote:
> Could you keep track of success?
>
> result_dict = dict()
> for id in taxid_list:
> result_dict[id] = False
> while not all(result_dict.values()): # continue if not every ID was
> successful
> for id in taxid_list:
> if res
> I am using the following code to submit the query/
> def get_BLAST(taxid, queryseq, args=None):
> '''
> Input taxid to BLAST queryseq against
> '''
> e_query = "txid" + taxid + " [ORGN]"
> #, other_advanced='-G 4 -E 1'
> blast_result = NCBIWWW.qblast("blastn", "nt", querys
I am using biopython's NCBIWWW.qblast which sends a request to the ncbi
website and waits for a result. The relevant code can be found at the link
below starting at about 151. Basically it is a while loop waiting for the
blast query.
http://biopython.org/DIST/docs/api/Bio.Blast.NCBIWWW-pysrc.html
