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POMultiple mismatches in DNA search sequence regex
 

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  1. POMultiple mismatches in DNA search sequence regex
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    <p>I have written this barbaric script to create permutations of a string of characters that contain n (up to n=4) $'s in all possible combinations of positions within the string. I will eventually <code>.replace('$','(\\w)')</code> to use for mismatches in a dna search sequence. Because of the way I wrote the script, some of the permutations have less than the requested number of $'s. I then wrote a script to remove them, but it doesn't seem to be effective, and each time I run the removal script, it removes more of the unwanted permutations. In the code pasted below, you will see that I test the function with a simple sequence with 4 mismatches. I then run a series of removal scripts that count how many expressions are removed each time...in my experience, it takes about 8 times to remove all expressions with less than 4 wild-card $'s. I have a couple questions about this:</p> <ol> <li><p>Is there a built in function for searches with 'n' mismatches? Maybe even in biopython? So far, I've seen the Paul_McGuire_regex function:<br> <a href="https://stackoverflow.com/questions/2420412/search-for-string-allowing-for-one-mismatch-in-any-location-of-the-string">Search for string allowing for one mismatch in any location of the string</a>,<br> which seems only to generate 1 mismatch. I must admit, I don't fully understand all of the code in the remainining functions on that page, as I am a very new coder.</p></li> <li><p>Since I see this as a good exercise for me, is there a better way to write this entire script?...Can I iterate Paul_McGuire_regex function as many times as I need?</p></li> <li><p>Most perplexing to me, why won't the removal script work 100% the first time?</p></li> </ol> <p>Thanks for any help you can provide!</p> <pre><code>def Mismatch(Search,n): List = [] SearchL = list(Search) if n &gt; 4: return("Error: Maximum of 4 mismatches") for i in range(0,len(Search)): if n == 1: SearchL_i = list(Search) SearchL_i[i] = '$' List.append(''.join(SearchL_i)) if n &gt; 1: for j in range (0,len(Search)): if n == 2: SearchL_j = list(Search) SearchL_j[i] = '$' SearchL_j[j] = '$' List.append(''.join(SearchL_j)) if n &gt; 2: for k in range(0,len(Search)): if n == 3: SearchL_k = list(Search) SearchL_k[i] = '$' SearchL_k[j] = '$' SearchL_k[k] = '$' List.append(''.join(SearchL_k)) if n &gt; 3: for l in range(0,len(Search)): if n ==4: SearchL_l = list(Search) SearchL_l[i] = '$' SearchL_l[j] = '$' SearchL_l[k] = '$' SearchL_l[l] = '$' List.append(''.join(SearchL_l)) counter=0 for el in List: if el.count('$') &lt; n: counter+=1 List.remove(el) return(List) List_RE = Mismatch('abcde',4) counter = 0 for el in List_RE: if el.count('$') &lt; 4: List_RE.remove(el) counter+=1 print("Filter2="+str(counter)) </code></pre>
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