Talk:Retrieve nonmatching blast queries

Revision as of 09:53, 11 May 2009

re Discussion

Hmmm, perhaps the 'one record at a time' I talked about isn't any faster. Doing this

for record in NCBIXML.parse(open("BLAST_RESULTS.out", 'r')):
  recID = record.query.split()[0] 
  if recID in q_dict.keys():
    del q_dict[recID

takes ~ 30secs on my little laptop with the files I used for the recipe whereas the recipe version takes more like 20secs. Is there another way to do this?

I think the check on each BLAST record should be conditional (e.g. if record.alignments) in case the NCBI do give an empty record when there are no hits. I think they do this already when there is a single query. Peter