Replace characters at a list of indices in a python string/list

Question

I have a dictionary as follows:

s_dict = {'s' : 'ATGCGTGACGTGA'}

I want to change the string stored as the value of the dictionary for key 's' at positions 4, 6, 7 and 10 to h, k, p and r.

pos_change = {'s' : ['4_h', '6_k', '7_p', '10_r']}

The way I can think about it is in a loop:

for key in s_dict:
    for position in pos_change[key]:
        pos = int(position.split("_")[0])
        char = position.split("_")[1]
        l = list(s_dict[key])
        l[pos]= char
        s_dict[key] = "".join(l)

Output:

s_dict = {'s': 'ATGChTkpCGrGA'}

This works fine but my actual s_dict file is about 1.5 Gb. Is there a faster way of replacing a list of characters at specific indices in a string or list?

Thanks!

pos_change would be better as a dict of dicts (pos_change = {'s' : {4: 'h', 6: 'k', 7: 'p', 10: 'r'}}) — Ma0
– Ma0, Commented Aug 21, 2018 at 13:41
@Chris_Rands Oh, no I just want to replace SNPs with IUPAC characters. I just made an example for the sake of the python question. — Homap
– Homap, Commented Aug 21, 2018 at 13:43
s_dict['s'] = '%s%s%s' % (s_dict['s'][:pos], char, s_dict['s'][pos+1:]) instead of do list and join — user8060120
– user8060120, Commented Aug 21, 2018 at 13:44

Ma0 · Accepted Answer · 2018-08-21 14:10:16Z

1

Here is my take on your interesting problem:

s_dict = {'s' : 'ATGCGTGACGTGA'}    
pos_change = {'s' : ['4_h', '6_k', '7_p', '10_r']}

# 1rst change `pos_change` into something more easily usable
pos_change = {k: dict(x.split('_') for x in v) for k, v in pos_change.items()}
print(pos_change)  # {'s': {'4': 'h', '6': 'k', '7': 'p', '10': 'r'}}

# and then... 
for k, v in pos_change.items():
  temp = set(map(int, v))
  s_dict[k] = ''.join([x if i not in temp else pos_change[k][str(i)] for i, x in enumerate(s_dict[k])])

print(s_dict)  # {'s': 'ATGChTkpCGrGA'}

answered Aug 21, 2018 at 14:10

Ma0

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score 1 · Accepted Answer · 2018-08-21 14:01:05Z

as an option of solution you can use s_dict['s'] = '%s%s%s' % (s_dict['s'][:pos], char, s_dict['s'][pos+1:]) instead of do list and join

In [1]: s_dict = {'s' : 'ATGCGTGACGTGA' * 10}
   ...: pos_change = {'s' : ['4_h', '6_k', '7_p', '10_r']}
   ...: 
   ...: def list_join():
   ...:     for key in s_dict:
   ...:         for position in pos_change[key]:
   ...:             pos = int(position.split("_")[0])
   ...:             char = position.split("_")[1]
   ...:             l = list(s_dict[key])
   ...:             l[pos]= char
   ...:             s_dict[key] = "".join(l)
   ...: 
   ...: def by_str():
   ...:     for key in s_dict:
   ...:         for position in pos_change[key]:
   ...:             pos = int(position.split("_")[0])
   ...:             char = position.split("_")[1]
   ...:             values = s_dict['s'][:pos], char, s_dict['s'][pos+1:]
   ...:             s_dict['s'] = '%s%s%s' % values
   ...:             

In [2]: %timeit list_join()
11.7 µs ± 191 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each)

In [3]: %timeit by_str()
4.29 µs ± 46.7 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each)

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