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Pull common probes from all methylation arrays and create a new store.
This is being done to allow for efficient selection of probes in a batch across tissues.



In [3]:

    
import pandas as pd



In [2]:

    
store = pd.HDFStore(METH_STORE)



In [11]:

    
idx = {}
for c in store.keys():
    if c in ['/matched_tn','/codes']:
        continue
    idx[c] = store[c].index
idx_common = reduce(set.intersection, map(set, idx.values()))
len(idx_common)









    Out[11]:





395883



In [17]:

    
for c in store.keys():
    if c in ['/matched_tn','/codes']:
        continue
    df = store[c]
    df.ix[idx_common].to_hdf(METH_STORE_MATCHED, c, format='t',
                             append=False, complevel=9)