Dear all, I want to delete a particular character in a string of one file, based on the corresponding scores in a different file. To explain the query in detail......

file number 1 - seq.txt
>s1
AGCTTTTCGGGCAAT
>s2
GCTGCCCCCCATCTT
>s3
TCGTAGCTGAAAATC

file number 2 - num.txt
>s1
23 43 45 65 76 54 3 34 54 65 7 45 56 87 56 
>s2
23 43 23 45 65 45 76 78 34 8 12 32 65 23 25
>s3
12 23 34 45 56 54 43 32 65 43 12 34 75 76 45


things to be done.

1) The sequence file and number file contains 
same number of enteries with same ID.

2) The number of nucleotides in a sequence in 
as same as the score of each nucleotide in the 
num.txt file.that is for example in seq.txt file, 
>s1 has 15 nucleotides, and in num.txt, >s1 has
15 scores for each corresponding nucleotide in 
the other file.

3) first thing to be checked is, if there is a 
repetition in the the bases(nucleotides). for 
this we can check only seq.txt file.for example: 
>s1 has 4 "T"  and 3 "G".....>s2 has 6 "C"......
and >s3 has 4 "A"..... 

4) we have to consider it as repeats only if the 
bases are continously 3 or more times. for example, 
in >s1 there is a 2 times "A" near the end of the sequence.....in >s2 
+there is a 2 times "T" at the 
end...these should not be taken as repeated bases. 

5) Once we choose the repeated bases according to 
point number (step 3), we have to take the 
corresponding ID in the num.txt file.

6) Example: 
-open seq.txt and open num.txt

-process >s1 in both the files.

-positions 4-7 is the repeat... "TTTT" 
in this case.

-the corresponding scores in position 4-7 
is "65 76 54 3"

-there fore its T   T   T   T
                65  76  54  3

-we have to check only the last base SCORE.

-If it is less than 10, we have to delete the score and nucleotide.

-hence the result sequence should be 


>s1
AGCTTTCGGGCAAT

>s1
23 43 45 65 76 54 34 54 65 7 45 56 87 56 

This has to be done for all the sequences 
in the file. >s3 wil not have any change coz, 
the last base of the repeat is more than 10. 
-----------------------------------------------------------
sooooooo, my SAMPLE RESULT FILE for 
the above input should look like:

file number 1 - seq.txt
>s1
AGCTTTCGGCAAT
>s2
GCTGCCCCCATCTT
>s3
TCGTAGCTGAAAATC

file number 2 - num.txt
>s1
23 43 45 65 76 54 34 54 65 45 56 87 56 
>s2
23 43 23 45 65 45 76 78 34 12 32 65 23 25
>s3
12 23 34 45 56 54 43 32 65 43 12 34 75 76 45
----------------------------------------------
[download]

Also, is it possible to find the position where we delete the character?

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