In the file below I am trying to count the given repeats of A,T,C,G in each string of letters. Each sequence is below the > and it is possible for a string of repeats to wrap from the line above. For example, in the first line the last letter is a T and the next lines has 3 more. I think the below would work, but I am also trying to count the position range of the repeat using the range=, where the first # represents the leftmost (in the first line that is aaa) and the second # rightmost (in the first line that is taa). So using the 4T as an example the output is in the example output.
The t{4} is the repeat that can change, for example if I am after 7g then that would be g{7}... the lower case letters in the sequence are counted along with the capital letters if they satisfy the criteria. I think both would be captured in the order there are seen, as that is important to know. For example, 4t occurs at chr2:166911127-166911130... even though there are 6t in that strech only the 4t satisfy the criteria and are counted. An example output is in the output for two sequences. Thank you .
file
example output
description
perl
output for two sequences
Last edited by cmccabe; 08-18-2018 at 01:33 PM..
Reason: fixed format
Thank you @Aia, your perl is much more complete than mine. Can the header be included with each sequence and if there is no repeat in that sequence Nothing Detected results? Thank you very much .
The line in green, specifically the tT{4}, is what I manually change to capture the different stretches of aA, tT, cC, gG stretches from 6-25. Is there a way to loop through the below possibilities, each changing automatically? It is always these combinations of letters only the length of the repeat changes. So, if I was capturing [aA]{8}/g for 8a/A or [aA]{18}/g for 18a/A. Thank you very much for your help I really appreciate it.
Looking into the data there are a couple of modifications that I am unsure how to incorporate. The streches are detected and the loop is amazing and very helpful. The math is slightly different and the repeat stretch is opposite, hopefully the examples will help to show but if strand=- then the bases in blue (rightmost) are the start or first number after the : and the repeats in green are opposite:
Thank you very much .
input
desired output
In the line with > if the strand=+ then everything is good except that the calculated range=chr2:166170446-166170451 is 1 digit off. An example is
is
In the line with > if the strand=- then the math is slightly different in that the first # is really the end position. An example is,
is
If Nothing Detected then the line is as is. Thank you again .
Last edited by cmccabe; 08-21-2018 at 05:05 PM..
Reason: added details
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