Find all occurances of a substring with python separated by max distance

Question

I'd like to match all occurances of a substring with python.

I found this, but I'd like to match occurances of a substring separated by at most some distance (for example maximum of 6). So if I have string

AATCGTGCCGTGTGCCCCAAAATGAACGCGCCGCTGTG

I want to get all positions of TG if two TG's are separated by at most 6 characters. So in the example above I'd like to get [5, 10, 12, 34, 36]. I don't want the middle TG positions, because it is too far away from either "group" (for 10 characters).

I tried with this:

(?=TG(?:.+){1,6}?)

but it doesn't work.

EDIT

I created regex that returns all the positions I want, except the last ones.

(?=TG.{0,6}TG)

If I use example above, returned positions are marked with |

AATCG|TGCCG|TGTGCCCCAAAATGAACGCGCCGC|TGTG

but I'd like to get also positions marked with \

AATCG|TGCCG|TG\TGCCCCAAAATGAACGCGCCGC|TG\TG

I know why it doesn't work, because it matches all TG followed by 0-6 random characters and one more TG, but I cannot get the idea what should I add to make it work.

" if distance between two TG's are maximum 6" - please clarify. Again, your example contradicts the description. — Karoly Horvath, Dec 06 '15 at 20:10
I want to get positions of TG separated by at most _some distance_. For example 6. So I want first three TGs in the final list, because they are separated for less than 6 characters (in first example they are 5 characters away and in second they are 2). At the end TGs are also separated by 2 characters. — thecoparyew, Dec 06 '15 at 20:22
@JoshCaswell to do it with one line. I don't know how to do it with one line if using `str.find`. — thecoparyew, Dec 06 '15 at 20:23

score 1 · Answer 1 · 2015-12-06T20:41:23.897

If using a regex, I think this should work.
The position has to be obtained from the position of capture group 1.

Note - I think your position 34 is not valid.

(?:^.*?|(?<=TG).{0,4})(TG)

Edit:

You can also do it this way to get the start of a new group of TG's.

Using \K - no capture groups: (?:(?<=TG).{0,4}\KTG|.*?\KTG(?=.{0,4}TG))
Formatted:

 (?:
      (?<= TG )
      .{0,4} 
      \K 
      TG
   |  
      .*? 
      \K 
      TG
      (?= .{0,4} TG )
 )

Without Branch Reset - 2 capture groups: (?:(?<=TG).{0,4}(TG)|.*?(TG)(?=.{0,4}TG))
Formatted:

 (?:
      (?<= TG )
      .{0,4} 
      ( TG )                        # (1)
   |  
      .*? 
      ( TG )                        # (2)
      (?= .{0,4} TG )
 )

With Branch Reset - 1 capture group: (?|(?<=TG).{0,4}(TG)|.*?(TG)(?=.{0,4}TG))

Formatted:

 (?|
      (?<= TG )
      .{0,4} 
      ( TG )                        # (1)
   |  
      .*? 
      ( TG )                        # (1)
      (?= .{0,4} TG )
 )

score 1 · Answer 2 · answered Dec 06 '15 at 20:44

You could do something like this, where you first find all the occurences, and then check the distance between indexes afterwards:

text = AATCGTGCCGTGTGCCCCAAAATGAACGCGCCGCTGTG
positions = []
index = 0

# Get all positions
while index < len(text):
    index = text.find('TG', index)
    positions.append(index)
    index += 2 # +2 because len('TG') == 2

# Filter out positions where distance are maximum 6
for i in range(1,len(positions)):
    if(((positions[i] - positions[i-1]) > 6) and ((positions[i+1] - positions[i]) > 6)): # check distance in both directions
        del positions[i]

# print resulting list
print positions

I haven't checked it, but it should do the job.

Find all occurances of a substring with python separated by max distance

2 Answers2