[Tutor] number of mismatches in a string

[bob gailer]

On 3/2/2012 2:11 PM, Hs Hs wrote:
> Hi:
> I have the following table and I am interested in calculating mismatch 
> ratio. I am not completely clear how to do this and any help is deeply 
> appreciated.
>
> Length     Matches
> 77      24A0T9T36
> 71      25^T9^T37
> 60      25^T9^T26
> 62      42A19
>
>
> In length column I have length of the character string.
> In the second column I have the matches my reference string.
>
>
> In fist case, where 77 is length, in matches from left to right, first 
> 24 matched my reference string following by a extra character A, a 
> null (does not account to proble) and extra T, 9 matches, extra T and 
> 36 matches.  Totally there are 3 mismatches
>
> In case 2, I lost 2 characters (^ = loss of character compared to 
> reference sentence)   -
>
> TOMISAGOODBOY
> T^MISAGOOD^OY   (here I lost 2 characters)  = I have 2 mismatches
> TOMISAGOOODBOOY (here I have 2 extra characters O and O) = I have two 
> mismatches
>
>
> In case 4: I have 42 matches, extra A and 19 matches = so I have 1 
> mismatch
>
>
> How can that mismatch number from matches string.
> 1. I have to count how many A or T or G or C (believe me only these 4 
> letters will appear in this, i will not see Z or B or K etc)
> 2. ^T or ^A or ^G or ^C will also be a mismatch
>
>
> desired output:
>
> Length     Matches   mismatches
> 77      24A0T9T36    3
> 71      25^T9^T37     2
> 60      25^T9^T26     2
> 62      42A19             1
> 10      6^TTT1           3
>

I am sorry but I do not understand, and do not have the patience to wade 
through all the above in the hopes of gaining insight.

Perhaps you could restate the problem in a way that makes it crystal clear.

-- 
Bob Gailer
919-636-4239
Chapel Hill NC

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