Testing scipy.sparse matrices

Seeing how much space can be saved, if working with sparse data.

Testing worst case database sizes

In the worst case the database will be storing a single value for each pair of proteins. Saving this file is time consuming and even if it can be saved it might be impossible to index it.



In [1]:

    
cd ~/Documents/MRes/geneconversion/









    



/home/gavin/Documents/MRes/geneconversion



In [2]:

    
ls









    



gene2go  gene_info  human.Entrez.pickle  testgen.pickle



In [3]:

    
import pickle



In [4]:

    
f = open("human.Entrez.pickle")
ids = pickle.load(f)
f.close()



In [5]:

    
import itertools



In [7]:

    
sys.path.append("/home/gavin/Documents/MRes/opencast-bio/")
import ocbio.extract



In [20]:

    
cd /mnt/external/remotes/geneontology/









    



/mnt/external/remotes/geneontology



In [ ]:

    
db = ocbio.extract.openpairshelf("test.db")
for p in itertools.combinations(ids,2):
    db[p] = 1
db.close()



In [ ]:

    
print "something"



In [12]:

    
print len(ids)