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POpython recursion with bubble sort
 

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  1. POpython recursion with bubble sort
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    <p>So, i have this problem where i recieve 2 strings of letters ACGT, one with only letters, the other contain letters and dashes "-".both are same length. the string with the dashes is compared to the string without it. cell for cell. and for each pairing i have a scoring system. i wrote this code for the scoring system: for example: dna1: -ACA dna2: TACG the scoring is -1. (because dash compared to a letter(T) gives -2, letter compared to same letter gives +1 (A to A), +1 (C to C) and non similar letters give (-1) so sum is -1.</p> <pre><code>def get_score(dna1, dna2, match=1, mismatch=-1, gap=-2): """""" score = 0 for index in range(len(dna1)): if dna1[index] is dna2[index]: score += match elif dna1[index] is not dna2[index]: if "-" not in (dna1[index], dna2[index]): score += mismatch else: score += gap </code></pre> <p>this is working fine.</p> <p>now i have to use recursion to give the best possible score for 2 strings. i recieve 2 strings, they can be of different sizes this time. ( i cant change the order of letters). so i wrote this code that adds "-" as many times needed to the shorter string to create 2 strings of same length and put them in the start of list. now i want to start moving the dashes and record the score for every dash position, and finally get the highest posibble score. so for moving the dashes around i wrote a litle bubble sort.. but it dosnt seem to do what i want. i realize its a long quesiton but i'd love some help. let me know if anything i wrote is not understood.</p> <pre><code>def best_score(dna1, dna2, match=1, mismatch=-1, gap=-2,\ score=[], count=0): """""" diff = abs(len(dna1) - len(dna2)) if len(dna1) is len(dna2): short = [] elif len(dna1) &lt; len(dna2): short = [base for base in iter(dna1)] else: short = [base for base in iter(dna2)] for i in range(diff): short.insert(count, "-") for i in range(diff+count, len(short)-1): if len(dna1) &lt; len(dna2): score.append((get_score(short, dna2),\ ''.join(short), dna2)) else: score.append((get_score(dna1, short),\ dna1, ''.join(short))) short[i+1], short[i] = short[i], short[i+1] if count is min(len(dna1), len(dna2)): return score[score.index(max(score))] return best_score(dna1, dna2, 1, -1, -2, score, count+1) </code></pre>
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    1. USDavid
    1. USDavid
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    1. COJust to clarify, it looks like you are trying to find the best possible place (defined as the highest score) to insert the sequence of dashes into the shorter DNA string, where all of the dashes are adjacent?
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      1. USBrett Lempereur
    2. COthe dashes are inserted by me incase 1 string is shorter than the other. so basically you are right, i need to find the optimal place for the dashes to get the highest score. i figure that if i place them in the start i could move the rightmost dash each step untill the end via bubble sort, and then reset the dashes and move them 1 cell forward and repeast the process. that way i record all possible scores and return the highest. incase the strings are same size i dont have to insert dashes. that case solves with the first function because there is only 1 possible score for it.. nothing moves.
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      1. USDavid
    3. COfor example: TCAATTAGCTT', 'TATA' are the 2 strings. i insert the dashes to right untill its same length and then move them around inside the right string for optimal score according to rules. i cant change the order of letters.
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