converting dictionary of dictionaries in python into numpy array in python [duplicate]

Question

I have a dictionary of dictionaries in python like the following example:

example:

result = {
    1: {'A': 11472, 'C': 8405, 'T': 11428, 'G': 6613}, 
    2: {'A': 11678, 'C': 9388, 'T': 10262, 'G': 6590}, 
    3: {'A': 2945, 'C': 25843, 'T': 6980, 'G': 2150}, 
    4: {'A': 1149, 'C': 24552, 'T': 7000, 'G': 5217}, 
    5: {'A': 27373, 'C': 3166, 'T': 4494, 'G': 2885}, 
    6: {'A': 19300, 'C': 4252, 'T': 7510, 'G': 6856}, 
    7: {'A': 17744, 'C': 5390, 'T': 7472, 'G': 7312}
}

and I want to make a numpy array in python using the values of inner dictionaries. in fact in the example there are 7 inner dictionaries with 4 items so, in the array thet would be 7 lists with 4 items. so, every item in the in the numpy array is one of the values in the inner dictionaries. for instance this is the 1st inner dictionary:

{'A': 11472, 'C': 8405, 'T': 11428, 'G': 6613}

and this would be the 1st list in the numpy array:

[ 11472,  8405,  11428,  6613]

I am trying to do that in python using the following line but it does not return expected output.

import pandas as pd
df = pandas.DataFrame(result, index=[0])

do you know how to fix it?

here is the expected output:

array([[ 11472,  8405,  11428,  6613],
       [ 11678,  9388,  10262 ,  6590],
       [ 2945,  25843,  6980 ,  2150],
       [ 1149,  24552,  7000 ,  5217],
       [ 27373,  3166,  4494 ,  2885],
       [ 19300,  4252,  7510,  6856],
       [ 17744,  5390,  7472,  7312]])

ForceBru · Accepted Answer · 2019-01-06 21:53:05Z

1

Requires Python 3. Also, the values must be inserted in the ACTG order.

>>> np.array([list(val.values()) for val in result.values()])
array([[11472,  8405, 11428,  6613],
       [11678,  9388, 10262,  6590],
       [ 2945, 25843,  6980,  2150],
       [ 1149, 24552,  7000,  5217],
       [27373,  3166,  4494,  2885],
       [19300,  4252,  7510,  6856],
       [17744,  5390,  7472,  7312]])

answered Jan 6, 2019 at 21:53

ForceBru

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5 Comments

elly Over a year ago

in python 2.7 also works.

Stephen Rauch Over a year ago

Dicts are not order in python 2.7

iz_ Over a year ago

@StephenRauch Dicts weren't ordered prior to Python 3.7, either.

Stephen Rauch Over a year ago

@Tomothy32, very true, except for CPython got a jump on the rest... :-)

iz_ Over a year ago

@StephenRauch That's true, except in 3.6 it was considered an "implementation detail and should not be relied upon".

Stephen Rauch · Accepted Answer · 2019-01-06 21:54:42Z

A couple of comprehensions can do that like:

Code:

data = [[result[idx][k] for k in 'ACTG']
        for idx in sorted(result)
        ]

an_array = np.array(data)

Test Code:

result = {1: {'A': 11472, 'C': 8405, 'T': 11428, 'G': 6613},
          2: {'A': 11678, 'C': 9388, 'T': 10262, 'G': 6590},
          3: {'A': 2945, 'C': 25843, 'T': 6980, 'G': 2150},
          4: {'A': 1149, 'C': 24552, 'T': 7000, 'G': 5217},
          5: {'A': 27373, 'C': 3166, 'T': 4494, 'G': 2885},
          6: {'A': 19300, 'C': 4252, 'T': 7510, 'G': 6856},
          7: {'A': 17744, 'C': 5390, 'T': 7472, 'G': 7312}}

data = [[result[idx][k] for k in 'ACTG']
        for idx in sorted(result)
        ]

print(data)

Results:

[[11472, 8405, 11428, 6613], 
 [11678, 9388, 10262, 6590], 
 [2945, 25843, 6980, 2150], 
 [1149, 24552, 7000, 5217], 
 [27373, 3166, 4494, 2885], 
 [19300, 4252, 7510, 6856], 
 [17744, 5390, 7472, 7312]]

thanks. this one returns a list of lists. but I want a numpy array. do you know how to do that?

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