|
| 1 | +{ |
| 2 | + "cells": [ |
| 3 | + { |
| 4 | + "cell_type": "code", |
| 5 | + "execution_count": null, |
| 6 | + "metadata": { |
| 7 | + "collapsed": true |
| 8 | + }, |
| 9 | + "outputs": [], |
| 10 | + "source": [ |
| 11 | + "def jaccard_distance(seq1, seq2):\n", |
| 12 | + " set1, set2 = set(seq1), set(seq2)\n", |
| 13 | + " return 1 - len(set1 & set2) / float(len(set1 | set2))" |
| 14 | + ] |
| 15 | + }, |
| 16 | + { |
| 17 | + "cell_type": "code", |
| 18 | + "execution_count": null, |
| 19 | + "metadata": { |
| 20 | + "collapsed": true |
| 21 | + }, |
| 22 | + "outputs": [], |
| 23 | + "source": [ |
| 24 | + "def sorensen_distance(seq1, seq2):\n", |
| 25 | + " set1, set2 = set(seq1), set(seq2)\n", |
| 26 | + " return 1 - (2 * len(set1 & set2) / float(len(set1) + len(set2)))" |
| 27 | + ] |
| 28 | + }, |
| 29 | + { |
| 30 | + "cell_type": "code", |
| 31 | + "execution_count": null, |
| 32 | + "metadata": { |
| 33 | + "collapsed": true |
| 34 | + }, |
| 35 | + "outputs": [], |
| 36 | + "source": [ |
| 37 | + "def hamming_distance(seq1, seq2, normalized = False):\n", |
| 38 | + " L = len(seq1)\n", |
| 39 | + " if L != len(seq2):\n", |
| 40 | + " raise ValueError(\"expected two strings of the same length\")\n", |
| 41 | + " if L == 0:\n", |
| 42 | + " return 0.0 if normalized else 0 # equal\n", |
| 43 | + " dist = sum(c1 != c2 for c1, c2 in zip(seq1, seq2))\n", |
| 44 | + " if normalized:\n", |
| 45 | + " return dist / float(L)\n", |
| 46 | + " return dist" |
| 47 | + ] |
| 48 | + } |
| 49 | + ], |
| 50 | + "metadata": { |
| 51 | + "kernelspec": { |
| 52 | + "display_name": "Python 3", |
| 53 | + "language": "python", |
| 54 | + "name": "python3" |
| 55 | + }, |
| 56 | + "language_info": { |
| 57 | + "codemirror_mode": { |
| 58 | + "name": "ipython", |
| 59 | + "version": 3 |
| 60 | + }, |
| 61 | + "file_extension": ".py", |
| 62 | + "mimetype": "text/x-python", |
| 63 | + "name": "python", |
| 64 | + "nbconvert_exporter": "python", |
| 65 | + "pygments_lexer": "ipython3", |
| 66 | + "version": "3.5.1" |
| 67 | + } |
| 68 | + }, |
| 69 | + "nbformat": 4, |
| 70 | + "nbformat_minor": 1 |
| 71 | +} |
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