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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,331 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# define a new sequence\n", | ||
| "seq = 'ACGT'" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# define a new sequence\n", | ||
| "seq = \"ACGT\"" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'C'" | ||
| ] | ||
| }, | ||
| "execution_count": 4, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# Get a character from a string\n", | ||
| "seq[1]" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "4" | ||
| ] | ||
| }, | ||
| "execution_count": 5, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# get the length of a sequence\n", | ||
| "len(seq)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# empty string (epsilon)\n", | ||
| "e = ''" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "0" | ||
| ] | ||
| }, | ||
| "execution_count": 7, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "len(e)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 8, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "AACCGGTT\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# concatenation\n", | ||
| "seq1 = 'AACC'\n", | ||
| "seq2 = 'GGTT'\n", | ||
| "print(seq1 + seq2)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 9, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "ACGT\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "seqs = ['A', 'C', 'G', 'T']\n", | ||
| "print(''.join(seqs))" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 10, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'T'" | ||
| ] | ||
| }, | ||
| "execution_count": 10, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# generate a random nucleotide\n", | ||
| "import random\n", | ||
| "random.choice('ACGT')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 14, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "CAAGTTATGC\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# generate a random sequence\n", | ||
| "seq = ''\n", | ||
| "for _ in range(10):\n", | ||
| " seq += random.choice('ACGT')\n", | ||
| "print(seq)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 15, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "GGCTCATTGA\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# another way to generate a random sequence\n", | ||
| "seq = ''.join([random.choice('ACGT') for _ in range(10)])\n", | ||
| "print(seq)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 16, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'GC'" | ||
| ] | ||
| }, | ||
| "execution_count": 16, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# get a substring\n", | ||
| "seq[1:3]" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 17, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'GGC'" | ||
| ] | ||
| }, | ||
| "execution_count": 17, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# get a prefix\n", | ||
| "seq[:3]" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 18, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'TGA'" | ||
| ] | ||
| }, | ||
| "execution_count": 18, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# get a suffix\n", | ||
| "seq[7:]" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 19, | ||
| "metadata": { | ||
| "collapsed": false | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "'TGA'" | ||
| ] | ||
| }, | ||
| "execution_count": 19, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "# another way to get a suffix\n", | ||
| "seq[-3:]" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.4.2" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 0 | ||
| } |
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