CG_001_StringBasics1.json

{
 "metadata": {
  "name": "CG_001_StringBasics1"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "'A'",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 1,
       "text": "'A'"
      }
     ],
     "prompt_number": 1
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "'ACGT'",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 2,
       "text": "'ACGT'"
      }
     ],
     "prompt_number": 2
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st = 'ACGT'",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 3
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "len(st) # getting the length of a string",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 6,
       "text": "4"
      }
     ],
     "prompt_number": 6
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "'' # empty string (epsilon)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 24,
       "text": "''"
      }
     ],
     "prompt_number": 24
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "len('')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 25,
       "text": "0"
      }
     ],
     "prompt_number": 25
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "import random\nrandom.choice('ACGT') # generating a random nucleotide",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 7,
       "text": "'T'"
      }
     ],
     "prompt_number": 7
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "random.choice('ACGT') # repeated invocations might yield different nucleotides",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 8,
       "text": "'G'"
      }
     ],
     "prompt_number": 8
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "random.choice('ACGT') # repeated invocations might yield different nucleotides",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 9,
       "text": "'G'"
      }
     ],
     "prompt_number": 9
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "random.choice('ACGT') # repeated invocations might yield different nucleotides",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 10,
       "text": "'G'"
      }
     ],
     "prompt_number": 10
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "random.choice('ACGT') # repeated invocations might yield different nucleotides",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 11,
       "text": "'C'"
      }
     ],
     "prompt_number": 11
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "# now I'll make a random nucleotide string by concatenating random nucleotides\nst = ''.join([random.choice('ACGT') for _ in xrange(40)])\nst",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 13,
       "text": "'CTACATACGACAAGTCTTCGAAAGAGCCTATCAATTGCTC'"
      }
     ],
     "prompt_number": 13
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st[1:3] # substring, starting at position 1 and extending up to but not including position 3\n# note that the first position is numbered 0",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 15,
       "text": "'TA'"
      }
     ],
     "prompt_number": 15
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st[0:3] # prefix of length 3",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 16,
       "text": "'CTA'"
      }
     ],
     "prompt_number": 16
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st[:3] # another way of getting the prefix of length 3",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 17,
       "text": "'CTA'"
      }
     ],
     "prompt_number": 17
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st[len(st)-3:len(st)] # suffix of length 3",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 18,
       "text": "'CTC'"
      }
     ],
     "prompt_number": 18
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st[-3:] # another way of getting the suffix of length 3",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 19,
       "text": "'CTC'"
      }
     ],
     "prompt_number": 19
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st1, st2 = 'CAT', 'ATAC'",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 20
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st1",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 21,
       "text": "'CAT'"
      }
     ],
     "prompt_number": 21
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st2",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 22,
       "text": "'ATAC'"
      }
     ],
     "prompt_number": 22
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "st1 + st2 # concatenation of 2 strings",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 23,
       "text": "'CATATAC'"
      }
     ],
     "prompt_number": 23
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "",
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}