Trying to create Numpy matrix/array but my output adds a \t and \n in python after splitting the comma separated array of numbers

Question

So I am trying to make a Numpy Array based on this set of numbers I have that is without a header and split based on space (my objective is to remove the arrays with ALL zeroes). this is the code I have:

with open('/Users/name/Desktop/PDB/test_d3psm_misc/d3ps.profile','r') as f:
    for line in f:
        r = line.split(" ")
        print(r)

my output:

['0.1\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.36\t0.54\t0.0\t0.0\t0.0\t\n']
['0.0\t0.06\t0.0\t0.0\t0.0\t0.0\t0.03\t0.0\t0.0\t0.0\t0.0\t0.0\t0.91\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\n']
['0.0\t0.0\t0.0\t0.0\t0.0\t0.02\t0.02\t0.0\t0.0\t0.51\t0.16\t0.06\t0.07\t0.0\t0.0\t0.0\t0.03\t0.0\t0.03\t0.1\t\n']
['0.02\t0.0\t0.05\t0.74\t0.0\t0.0\t0.12\t0.0\t0.0\t0.0\t0.0\t0.01\t0.0\t0.0\t0.03\t0.03\t0.0\t0.0\t0.0\t0.0\t\n']
['0.18\t0.1\t0.05\t0.13\t0.01\t0.0\t0.02\t0.04\t0.05\t0.0\t0.02\t0.13\t0.0\t0.09\t0.1\t0.06\t0.01\t0.0\t0.0\t0.0\t\n']
['0.04\t0.01\t0.07\t0.27\t0.04\t0.0\t0.12\t0.0\t0.0\t0.0\t0.26\t0.08\t0.0\t0.0\t0.01\t0.01\t0.03\t0.0\t0.01\t0.06\t\n']
['0.0\t0.04\t0.01\t0.02\t0.0\t0.01\t0.02\t0.46\t0.0\t0.0\t0.0\t0.05\t0.0\t0.0\t0.21\t0.13\t0.02\t0.0\t0.03\t0.0\t\n']
['0.02\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.11\t0.02\t0.04\t0.03\t0.0\t0.15\t0.0\t0.0\t0.0\t0.0\t0.64\t0.0\t\n']
['0.0\t0.79\t0.0\t0.0\t0.0\t0.03\t0.0\t0.0\t0.01\t0.0\t0.02\t0.12\t0.0\t0.0\t0.0\t0.0\t0.02\t0.0\t0.0\t0.0\t\n']
['0.05\t0.02\t0.01\t0.0\t0.02\t0.07\t0.01\t0.0\t0.0\t0.05\t0.04\t0.09\t0.01\t0.0\t0.46\t0.02\t0.09\t0.0\t0.0\t0.05\t\n']
['0.03\t0.11\t0.31\t0.0\t0.24\t0.0\t0.0\t0.21\t0.02\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.03\t0.02\t0.0\t0.0\t0.04\t\n']
['0.08\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.09\t0.0\t0.0\t0.0\t0.0\t0.05\t0.02\t0.0\t0.0\t0.01\t0.74\t\n']
['0.2\t0.0\t0.02\t0.0\t0.01\t0.0\t0.0\t0.59\t0.02\t0.02\t0.0\t0.0\t0.0\t0.01\t0.0\t0.06\t0.03\t0.0\t0.0\t0.01\t\n']
['0.17\t0.0\t0.02\t0.0\t0.04\t0.0\t0.0\t0.05\t0.0\t0.45\t0.04\t0.0\t0.06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.16\t\n']
['0.07\t0.0\t0.0\t0.0\t0.09\t0.0\t0.0\t0.01\t0.0\t0.33\t0.06\t0.0\t0.08\t0.04\t0.0\t0.0\t0.0\t0.0\t0.0\t0.31\t\n']
['0.07\t0.0\t0.0\t0.0\t0.01\t0.0\t0.0\t0.0\t0.0\t0.2\t0.33\t0.0\t0.01\t0.03\t0.02\t0.0\t0.01\t0.0\t0.02\t0.29\t\n']
['0.07\t0.06\t0.0\t0.01\t0.1\t0.03\t0.02\t0.01\t0.0\t0.14\t0.18\t0.0\t0.07\t0.11\t0.0\t0.01\t0.04\t0.0\t0.02\t0.12\t\n']
['0.0\t0.09\t0.48\t0.13\t0.01\t0.01\t0.04\t0.0\t0.01\t0.02\t0.02\t0.02\t0.0\t0.0\t0.01\t0.07\t0.05\t0.0\t0.0\t0.04\t\n']
['0.07\t0.22\t0.03\t0.08\t0.0\t0.06\t0.12\t0.05\t0.05\t0.01\t0.01\t0.07\t0.02\t0.0\t0.04\t0.1\t0.03\t0.0\t0.02\t0.01\t\n']
['0.03\t0.1\t0.09\t0.16\t0.01\t0.12\t0.16\t0.04\t0.02\t0.0\t0.0\t0.12\t0.0\t0.01\t0.04\t0.03\t0.03\t0.0\t0.01\t0.03\t\n']
['0.01\t0.05\t0.13\t0.09\t0.01\t0.04\t0.02\t0.44\t0.0\t0.0\t0.0\t0.14\t0.01\t0.0\t0.02\t0.02\t0.0\t0.0\t0.0\t0.0\t\n']
['0.0\t0.1\t0.02\t0.03\t0.01\t0.23\t0.23\t0.01\t0.03\t0.01\t0.06\t0.19\t0.0\t0.0\t0.01\t0.01\t0.02\t0.0\t0.0\t0.02\t\n']
['0.01\t0.0\t0.0\t0.0\t0.01\t0.0\t0.05\t0.0\t0.0\t0.23\t0.15\t0.0\t0.01\t0.01\t0.0\t0.0\t0.0\t0.0\t0.0\t0.53\t\n']
['0.01\t0.0\t0.0\t0.0\t0.0\t0.0\t0.01\t0.0\t0.0\t0.05\t0.6\t0.01\t0.03\t0.21\t0.0\t0.0\t0.01\t0.05\t0.01\t0.01\t\n']
['0.03\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.13\t0.42\t0.0\t0.06\t0.0\t0.0\t0.0\t0.02\t0.15\t0.02\t0.17\t\n']
['0.28\t0.0\t0.0\t0.0\t0.01\t0.04\t0.01\t0.26\t0.0\t0.03\t0.06\t0.01\t0.01\t0.0\t0.01\t0.02\t0.11\t0.0\t0.0\t0.16\t\n']
['0.02\t0.4\t0.02\t0.0\t0.02\t0.19\t0.01\t0.02\t0.03\t0.0\t0.0\t0.21\t0.0\t0.0\t0.0\t0.07\t0.0\t0.0\t0.0\t0.0\t\n']
['0.02\t0.69\t0.02\t0.0\t0.0\t0.01\t0.05\t0.05\t0.01\t0.0\t0.01\t0.05\t0.0\t0.01\t0.0\t0.05\t0.0\t0.01\t0.01\t0.02\t\n']
['0.07\t0.02\t0.01\t0.01\t0.01\t0.05\t0.01\t0.0\t0.05\t0.11\t0.16\t0.08\t0.03\t0.09\t0.03\t0.08\t0.04\t0.01\t0.08\t0.05\t\n']
['0.07\t0.16\t0.05\t0.11\t0.02\t0.0\t0.02\t0.24\t0.06\t0.01\t0.01\t0.1\t0.01\t0.0\t0.05\t0.04\t0.0\t0.0\t0.01\t0.04\t\n']
['0.04\t0.05\t0.09\t0.08\t0.0\t0.15\t0.07\t0.04\t0.02\t0.02\t0.01\t0.12\t0.01\t0.0\t0.07\t0.1\t0.09\t0.0\t0.02\t0.01\t\n']
['0.01\t0.01\t0.11\t0.13\t0.0\t0.02\t0.04\t0.27\t0.19\t0.0\t0.01\t0.08\t0.0\t0.0\t0.04\t0.04\t0.01\t0.0\t0.04\t0.0\t\n']
['0.12\t0.06\t0.01\t0.01\t0.03\t0.04\t0.0\t0.03\t0.02\t0.04\t0.11\t0.02\t0.05\t0.03\t0.0\t0.19\t0.11\t0.01\t0.05\t0.08\t\n']
['0.0\t0.03\t0.0\t0.0\t0.0\t0.0\t0.0\t0.03\t0.01\t0.01\t0.03\t0.0\t0.01\t0.03\t0.01\t0.0\t0.0\t0.78\t0.06\t0.01\t\n']
['0.05\t0.0\t0.02\t0.03\t0.0\t0.33\t0.08\t0.07\t0.03\t0.03\t0.01\t0.06\t0.0\t0.03\t0.0\t0.11\t0.06\t0.0\t0.02\t0.06\t\n']
['0.03\t0.0\t0.0\t0.0\t0.02\t0.01\t0.0\t0.03\t0.0\t0.05\t0.2\t0.0\t0.13\t0.31\t0.05\t0.02\t0.02\t0.0\t0.02\t0.11\t\n']
['0.01\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.01\t0.0\t0.01\t0.06\t0.0\t0.0\t0.01\t0.82\t0.04\t0.0\t0.0\t0.0\t0.03\t\n']
['0.13\t0.02\t0.01\t0.0\t0.0\t0.28\t0.0\t0.34\t0.0\t0.0\t0.0\t0.15\t0.0\t0.0\t0.0\t0.02\t0.05\t0.0\t0.0\t0.0\t\n']
['0.0\t0.0\t0.03\t0.0\t0.0\t0.0\t0.0\t0.97\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\n']
['0.05\t0.08\t0.0\t0.0\t0.0\t0.0\t0.0\t0.39\t0.14\t0.0\t0.03\t0.12\t0.0\t0.12\t0.0\t0.02\t0.01\t0.0\t0.01\t0.02\t\n']
['0.03\t0.02\t0.0\t0.0\t0.05\t0.0\t0.0\t0.0\t0.0\t0.29\t0.1\t0.01\t0.08\t0.0\t0.04\t0.01\t0.01\t0.02\t0.0\t0.35\t\n']
['0.02\t0.01\t0.07\t0.23\t0.03\t0.02\t0.41\t0.03\t0.01\t0.01\t0.02\t0.09\t0.03\t0.0\t0.0\t0.02\t0.0\t0.0\t0.0\t0.01\t\n']
['0.07\t0.02\t0.01\t0.05\t0.0\t0.02\t0.12\t0.01\t0.01\t0.08\t0.03\t0.12\t0.0\t0.03\t0.27\t0.08\t0.01\t0.0\t0.02\t0.03\t\n']
['0.01\t0.01\t0.05\t0.17\t0.01\t0.0\t0.03\t0.63\t0.02\t0.0\t0.0\t0.01\t0.01\t0.0\t0.0\t0.05\t0.01\t0.0\t0.0\t0.01\t\n']
['0.01\t0.0\t0.0\t0.02\t0.0\t0.0\t0.9\t0.0\t0.01\t0.0\t0.05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\n']
['0.01\t0.02\t0.04\t0.11\t0.01\t0.01\t0.11\t0.0\t0.0\t0.0\t0.0\t0.02\t0.0\t0.0\t0.01\t0.31\t0.37\t0.0\t0.0\t0.0\t\n']
['0.1\t0.0\t0.01\t0.04\t0.0\t0.01\t0.01\t0.0\t0.0\t0.11\t0.15\t0.0\t0.01\t0.07\t0.37\t0.01\t0.02\t0.01\t0.03\t0.04\t\n']
['0.06\t0.05\t0.0\t0.01\t0.0\t0.04\t0.44\t0.02\t0.03\t0.04\t0.11\t0.03\t0.02\t0.01\t0.02\t0.02\t0.02\t0.04\t0.01\t0.03\t\n']
['0.11\t0.0\t0.01\t0.16\t0.0\t0.25\t0.3\t0.01\t0.01\t0.01\t0.01\t0.02\t0.0\t0.0\t0.01\t0.01\t0.05\t0.0\t0.01\t0.04\t\n']
['0.63\t0.0\t0.05\t0.0\t0.13\t0.0\t0.0\t0.07\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.02\t0.1\t0.0\t0.0\t0.0\t\n']
['0.44\t0.0\t0.0\t0.0\t0.01\t0.0\t0.0\t0.03\t0.0\t0.04\t0.11\t0.0\t0.12\t0.04\t0.0\t0.01\t0.0\t0.0\t0.0\t0.19\t\n']
['0.13\t0.06\t0.01\t0.0\t0.01\t0.03\t0.05\t0.0\t0.02\t0.08\t0.2\t0.05\t0.03\t0.05\t0.0\t0.01\t0.0\t0.01\t0.12\t0.14\t\n']
['0.0\t0.95\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\n']
['0.0\t0.05\t0.0\t0.0\t0.0\t0.0\t0.91\t0.0\t0.0\t0.0\t0.03\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\n']
['0.06\t0.0\t0.0\t0.0\t0.01\t0.0\t0.0\t0.01\t0.0\t0.1\t0.4\t0.0\t0.03\t0.02\t0.0\t0.02\t0.09\t0.0\t0.01\t0.25\t\n']
['0.02\t0.1\t0.02\t0.01\t0.01\t0.12\t0.08\t0.01\t0.04\t0.01\t0.07\t0.17\t0.03\t0.08\t0.03\t0.02\t0.0\t0.08\t0.1\t0.01\t\n']
['0.03\t0.0\t0.0\t0.0\t0.0\t0.0\t0.91\t0.0\t0.03\t0.0\t0.0\t0.0\t0.0\t0.03\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\n']
['0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\n']
['0.09\t0.0\t0.0\t0.0\t0.01\t0.0\t0.0\t0.01\t0.0\t0.11\t0.12\t0.0\t0.0\t0.0\t0.0\t0.09\t0.36\t0.0\t0.0\t0.22\t\n']
['0.03\t0.02\t0.03\t0.01\t0.0\t0.01\t0.0\t0.86\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.03\t0.01\t0.0\t0.0\t0.0\t\n']
['0.02\t0.0\t0.0\t0.0\t0.02\t0.0\t0.01\t0.0\t0.01\t0.25\t0.32\t0.0\t0.02\t0.04\t0.0\t0.02\t0.03\t0.0\t0.07\t0.18\t\n']
['0.03\t0.08\t0.06\t0.17\t0.01\t0.04\t0.07\t0.02\t0.03\t0.02\t0.04\t0.13\t0.01\t0.01\t0.04\t0.09\t0.09\t0.0\t0.01\t0.03\t\n']
['0.15\t0.03\t0.01\t0.01\t0.03\t0.03\t0.02\t0.07\t0.0\t0.07\t0.06\t0.08\t0.0\t0.01\t0.17\t0.03\t0.07\t0.0\t0.01\t0.16\t\n']
['0.04\t0.07\t0.04\t0.08\t0.01\t0.06\t0.27\t0.05\t0.03\t0.01\t0.03\t0.17\t0.0\t0.0\t0.02\t0.05\t0.04\t0.01\t0.0\t0.01\t\n']
['0.01\t0.03\t0.11\t0.16\t0.0\t0.05\t0.04\t0.01\t0.1\t0.02\t0.07\t0.08\t0.01\t0.05\t0.07\t0.12\t0.02\t0.0\t0.02\t0.04\t\n']
['0.04\t0.02\t0.0\t0.02\t0.01\t0.01\t0.02\t0.04\t0.0\t0.14\t0.13\t0.03\t0.01\t0.02\t0.02\t0.06\t0.03\t0.01\t0.02\t0.38\t\n']
['0.04\t0.21\t0.02\t0.02\t0.01\t0.08\t0.26\t0.01\t0.02\t0.02\t0.04\t0.07\t0.0\t0.0\t0.0\t0.07\t0.07\t0.0\t0.0\t0.04\t\n']
['0.01\t0.01\t0.03\t0.0\t0.0\t0.0\t0.0\t0.01\t0.0\t0.27\t0.22\t0.07\t0.01\t0.07\t0.01\t0.03\t0.0\t0.01\t0.1\t0.15\t\n']
['0.02\t0.01\t0.01\t0.01\t0.0\t0.0\t0.0\t0.01\t0.01\t0.2\t0.46\t0.0\t0.03\t0.07\t0.0\t0.02\t0.01\t0.01\t0.01\t0.13\t\n']
['0.28\t0.02\t0.02\t0.01\t0.0\t0.01\t0.04\t0.31\t0.01\t0.0\t0.02\t0.03\t0.0\t0.0\t0.02\t0.09\t0.06\t0.02\t0.02\t0.01\t\n']
['0.05\t0.1\t0.01\t0.02\t0.08\t0.06\t0.17\t0.04\t0.03\t0.03\t0.01\t0.08\t0.0\t0.04\t0.01\t0.14\t0.03\t0.0\t0.0\t0.11\t\n']
['0.05\t0.04\t0.01\t0.01\t0.02\t0.06\t0.02\t0.02\t0.01\t0.11\t0.06\t0.01\t0.02\t0.06\t0.02\t0.13\t0.23\t0.0\t0.04\t0.08\t\n']
['0.03\t0.22\t0.03\t0.03\t0.0\t0.08\t0.06\t0.01\t0.02\t0.01\t0.08\t0.14\t0.0\t0.02\t0.18\t0.03\t0.03\t0.0\t0.01\t0.02\t\n']
['0.03\t0.04\t0.06\t0.17\t0.04\t0.03\t0.1\t0.12\t0.02\t0.01\t0.03\t0.05\t0.0\t0.01\t0.14\t0.07\t0.02\t0.0\t0.05\t0.01\t\n']
['0.02\t0.02\t0.01\t0.03\t0.0\t0.01\t0.05\t0.01\t0.06\t0.01\t0.04\t0.03\t0.01\t0.04\t0.02\t0.04\t0.03\t0.52\t0.02\t0.02\t\n']
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['0.3\t0.1\t0.01\t0.0\t0.01\t0.03\t0.06\t0.03\t0.1\t0.05\t0.0\t0.04\t0.0\t0.01\t0.0\t0.17\t0.0\t0.0\t0.0\t0.09\t\n']
['0.07\t0.15\t0.06\t0.03\t0.0\t0.11\t0.07\t0.05\t0.04\t0.02\t0.0\t0.01\t0.01\t0.0\t0.17\t0.19\t0.02\t0.0\t0.0\t0.0\t\n']
['0.01\t0.02\t0.0\t0.0\t0.0\t0.02\t0.0\t0.0\t0.05\t0.07\t0.31\t0.0\t0.0\t0.27\t0.0\t0.03\t0.03\t0.01\t0.08\t0.08\t\n']
['0.19\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.01\t0.0\t0.15\t0.48\t0.05\t0.0\t0.03\t0.0\t0.01\t0.02\t0.0\t0.0\t0.07\t\n']
['0.01\t0.11\t0.01\t0.01\t0.19\t0.16\t0.0\t0.01\t0.0\t0.05\t0.1\t0.03\t0.1\t0.15\t0.0\t0.01\t0.0\t0.0\t0.0\t0.05\t\n']
['0.23\t0.04\t0.05\t0.09\t0.0\t0.02\t0.0\t0.04\t0.02\t0.0\t0.0\t0.0\t0.0\t0.0\t0.24\t0.29\t0.0\t0.0\t0.0\t0.0\t\n']
['0.13\t0.0\t0.0\t0.0\t0.0\t0.06\t0.05\t0.02\t0.02\t0.04\t0.24\t0.0\t0.05\t0.1\t0.04\t0.0\t0.11\t0.0\t0.0\t0.15\t\n']
['0.44\t0.02\t0.0\t0.0\t0.0\t0.18\t0.09\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.19\t0.02\t0.02\t0.0\t0.0\t0.03\t\n']
['0.51\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.3\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.19\t0.0\t0.0\t0.0\t0.0\t\n']

I dont understand why this is happening. If there is an easier why to parse a bunch of files with numbers in it finding those that are ALL zeroes that would be better :)

Salvatore Daniele Bianco · Accepted Answer · 2022-01-27T11:57:46.780

1

import pandas as pd

df = pd.read_csv("/Users/name/Desktop/PDB/test_d3psm_misc/d3ps.profile", sep="\t", header=None).astype(float)
df = df.loc[df.sum(axis=1)>0]

Then, if you want to convert in numpy array:

df = df.to_numpy()

edited Jan 27 '22 at 11:57

answered Jan 27 '22 at 11:52

Salvatore Daniele Bianco

2,496
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Thank you! The .astype(Float), could you explain that part please? And also the (sum(axis=1)>0] portion – Francesca C Jan 27 '22 at 13:17
@fsc8907 `astype(float)` converts your data in float numbers; I think that in your case is not necessary, but I wanted to be sure. In the second line you sum the numbers in the same row (`axis=1` means that you want to sum along the columns axis, preserving the number of rows) and if this sum is > 0 (meaning there is at least one positive number) you take that row. Note that this algorithm may not work if there are some negative numbers in your data. – Salvatore Daniele Bianco Jan 27 '22 at 14:24
Thank you kindly! Makes perfect sense....but what if I want to select those that are equal to zero? Cause what I am doing is taking checkpoint files that look like the photo in my post here: [link](https://stackoverflow.com/questions/70895269/output-is-an-empty-file?noredirect=1#comment125332188_70895269) and filtering just those that have the zero in the profile portion, so that I can remove it from the dataset! – Francesca C Jan 28 '22 at 15:14
@FrancescaC sorry i didn't properly understand what is the output your are interested in. Do you need in output the indexes of the all-zeros columns? – Salvatore Daniele Bianco Jan 28 '22 at 15:58

Trying to create Numpy matrix/array but my output adds a \t and \n in python after splitting the comma separated array of numbers

1 Answers1