adding a zero at first element in a numpy array or a way to create an array keeping the first position as zero

Question

I got this function to looking for some specific characters in a string and if it is found it add a value at that position in the array, ex:

def skew_array(text):
    import numpy as np
    skew = np.zeros(len(text))
    for i in range(0, len(text)):
        if text[i] == 'G':
            skew[i] += 1
        elif text[i] == 'C':
            skew[i] -= 1
        else:
            skew[i] = 0
    return np.insert(skew, 0, 0)

>> skew_array('gacaattagcaa'.upper())
array([ 0.,  1.,  0., -1.,  0.,  0.,  0.,  0.,  0.,  1., -1.,  0.,  0.])

I am not sure if it is the right way to do it (inserting at the end) or if there are a way just to keep the first position as zero when creating the array.

I appreciate any tip! Thank you by your time.

PS - I was using a list, but it is very bad for memory in bigger strings!

2 revs · Accepted Answer · 2021-11-09 13:48:29Z

1

i think that functions that change the flat size of arrays are pretty slow, so i'd create skew larger from the start. and you can use a dict to avoid an elif soup

import numpy as np
def skew_array(text, dict_):
    skew = np.zeros(len(text)+1)
    for i, char in enumerate(text, start=1):
        skew[i] = dict_.get(char, 0)
    return skew

skew_dict={"G":1, "C":-1}
code='gacaattagcaa'.upper()
print(skew_array(code, skew_dict))

edited Nov 9, 2021 at 13:48

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2 revs
diggusbickus

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5 Comments

Reti43 Over a year ago

Since you need both the index and the value at said index, it would be better to loop with for i, char in enumerate(text, start=1). The dict could also contain only the keys for G and C and then fetch the value with dict.get(key, 0).

folen gateis Over a year ago

i always forgot about that start argument, thanks

Reti43 Over a year ago

Just to be clear, the dict suggestion is a preference. I just think leaving out any zero keys makes it less cumbersome to write and it's more apparent what has non-zero values. But for only 4 keys, initialising all 4 is also fine.

folen gateis Over a year ago

that's part of the things i always forget though they are very handy when we need them. so i'm really ok with that

Paulo Sergio Schlogl Over a year ago

That is very nice! Thanks

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