[Biopython] index_db problem

natassa natassa_g_2000 at yahoo.com
Tue Nov 15 12:28:16 UTC 2011


Hi, 

I have a problem with a script using the Bio.SeqIO index_db function: I have previously it successfully, but as I  had to recently change computers I now tried the same  script with no success. I get the error:

AttributeError: 'module' object has no attribute 'index_db'

although I have installed biopython 1.58 (the index_db is apparently from 1.57 and on, and on the pevious computer I had installed the 1.57). I checked if i have sqlite 3 by importing the module, and this seems OK. So now i am kind of stuck why the module SeqIO from 1.58 gets imported, but not the function. 


My function using it is something like:

def Sample_RandomHeader(numbRecs, reps, path):
  
    species=os.path.basename(path).split('_')[0].split('.')[0] 

    newdir=os.path.dirname(path)+'/'+species+str(numbRecs)+'_'+str(reps)+'Randoms/'
    speciesdb=SeqIO.index_db(species+'.idx', path, "fasta")  
....

and i have python 2.6

Any help would be appreciated!
Thank you, 

Anastasia




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