Replace a list of characters with indices in a string in python

Question

I have a list of coordinates:

coordinates = [[1,5], [10,15], [25, 35]]

I have a string as follows:

line = 'ATCACGTGTGTGTACACGTACGTGTGNGTNGTTGAGTGKWSGTGAAAAAKCT'

I want to replace intervals indicated in pairs in coordinates as start and end with character 'N'.

The only way I can think of is the following:

for element in coordinates:
 length = element[1] - element[0]
 line = line.replace(line[element[0]:element[1]], 'N'*length)

The desired output would be:

line = 'ANNNNGTGTGNNNNNACGTACGTGTNNNNNNNNNNGTGKWSGTGAAAAAKCT'

where intervals, [1,5), [10,15) and [25, 35) are replaced with N in line.

This requires me to loop through the coordinate list and update my string line, every time. I was wondering if there is another way that one can replace a list of intervals in a string?

Note: There is a problem with the original solution in this question. In line.replace(line[element[0]:element[1]], 'N'*length), replace will replace all other instances of string identical to the one in line[element[0]:element[1]] from the sequence and for people working with DNA, this is definitely not what you want! I however, keep the solution as it is to not disturb the flow of comments and discussion following.

• alani: Please add example (desired) output to the question.
• alani: But I think this should do what you want: for start, end in coordinates: line = line[:start] + "N" * (end - start) + line[end:] -- if I've correctly understood.
• Tomerikoo: I am not sure your current solution even does what you expect. replace replaces all occurrences of the sub-string so it might not only replace the indices you give it
• Homap: @Tomerikoo Oh, really, that's so important. It looks in my example is working correctly with the indices I give to it. How do you think it could cause a problem? Is there another method I could use instead?
• Tomerikoo: @Homap it might cause a problem if for example the substring between indices 1 and 5 (TCAC) appears somewhere else in the string, so it will be replaced as well. That might not be what you want

Answer 1

Instead of string concatenation (wich is wasteful due to created / destroyed string instances), use a list:

coordinates = [[1,5], [10,15], [25, 35]] # sorted
line = 'ATCACGTGTGTGTACACGTACGTGTGNGTNGTTGAGTGKWSGTGAAAAAKCT'
result = list(line)
# opted for exclusive end pos
for r in [range(start,end) for start,end in coordinates]:
 for p in r:
 result[p]='N'
res = ''.join(result)
print(res)

To get:

ANNNNGTGTGNNNNNACGTACGTGTNNNNNNNNNNGTGKWSGTGAAAAAKCT

---

optimized to use slicing and exclusive end:

for start,end in coordinates:
 result[start:end] = ["N"]*(end-start)
res = ''.join(result)
print(line)
print(res)

gives you your wanted output:

ATCACGTGTGTGTACACGTACGTGTGNGTNGTTGAGTGKWSGTGAAAAAKCT 
ANNNNGTGTGNNNNNACGTACGTGTNNNNNNNNNNGTGKWSGTGAAAAAKCT

• Homap: This solution took about 89 seconds on 2.4 GB file.

Answer 2

Good question, this should work.

coordinates = [[1,5], [10,15], [25, 35]]
line = 'ATCACGTGTGTGTACACGTACGTGTGNGTNGTTGAGTGKWSGTGAAAAAKCT'
for L,R in coordinates:
 line = line[:L] + "N"*(R-L) + line[R:]
print(line)

You may need to adjust this depending on how the coordinates are defined, eg. inclusive/1-indexed.

We need more people working with DNA, so great work.

• alani: Good. The code in the question would probably imply that the indices should be as you have now shown (and I thought the same - see my comment under the question) but some example output from the OP would certainly help clarify this.
• alani: Ah, now we have example output in the question, and it is as suspected.