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POLooking for elegant glob-like DNA string expansion
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copied!<p>I'm trying to make a glob-like expansion of a set of DNA strings that have multiple possible bases.</p> <p>The base of my DNA strings contains the letters A, C, G, and T. However, I can have special characters like M which could be an A or a C.</p> <p>For example, say I have the string:</p> <p><code>ATMM</code></p> <p>I would like to take this string as input and output the four possible matching strings:</p> <p><code>ATAA</code> <code>ATAC</code> <code>ATCA</code> <code>ATCC</code></p> <p>Rather than brute force a solution, I feel like there must be some elegant Python/Perl/Regular Expression trick to do this. </p> <p>Thank you for any advice.</p> <p><strong>Edit, thanks cortex for the product operator. This is my solution:</strong></p> <p>Still a Python newbie, so I bet there's a better way to handle each dictionary key than another for loop. Any suggestions would be great.</p> <pre><code>import sys from itertools import product baseDict = dict(M=['A','C'],R=['A','G'],W=['A','T'],S=['C','G'], Y=['C','T'],K=['G','T'],V=['A','C','G'], H=['A','C','T'],D=['A','G','T'],B=['C','G','T']) def glob(str): strings = [str] ## this loop visits very possible base in the dictionary ## probably a cleaner way to do it for base in baseDict: oldstrings = strings strings = [] for string in oldstrings: strings += map("".join,product(*[baseDict[base] if x == base else [x] for x in string])) return strings for line in sys.stdin.readlines(): line = line.rstrip('\n') permutations = glob(line) for x in permutations: print x </code></pre>

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