53 lines
1.2 KiB
Python
53 lines
1.2 KiB
Python
#!/usr/bin/python3
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"""
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Solutions to the PROB Rosalind Problem - Introduction to Random Strings
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Author: Peter Vlasveld
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Date: 20190222
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"""
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import math
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# Read in file content into list
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f1 = open("rosalind_prob.txt")
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content = f1.readlines()
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f1.close()
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"""
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Function to calculate the probability of the exact sequence given the
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GC-content
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@param gc - the GC-content given
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@param seq - the sequence being studied
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@return - the raw probability value
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"""
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def calcProb(gc, seq):
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# get probability for just one nucleotide
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gchalf = gc / 2.0
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athalf = (1.0 - gc) / 2.0
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# multiply all of the probability values for each letter in the sequence
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prob = 1.0
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for i in range(0, len(seq)):
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if seq[i] == "A" or seq[i] == "T":
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prob *= athalf
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elif seq[i] == "G" or seq[i] == "C":
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prob *= gchalf
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# return the probability value
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return prob
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# take the log of the probabilities returned by calcProb
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# format them to 3 decimal places
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gcCons = content[1].split()
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finalProbs = []
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for i in gcCons:
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rawProb = calcProb(float(i), content[0])
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finalProbs.append("%.3f" % math.log10(rawProb))
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# print the probabilities with spaces in between
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print(" ".join(finalProbs))
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