Randomization

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Randomization
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Randomization

• Most computer languages have a built in function
  to generate "random" numbers
• The numbers generated are not truly random but
  are considered "pseudo-random"
• For most purposes, these are good enough

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Randomization

• The PERL Random number must be "seeded" first
• PERL will seed the rand function for you if you
  do not explicit seed the generator yourself
• The command for seeding is
• srand(number)
• Once the random number generator is seeded, it
  will generate a series of random numbers

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Randomization

• PERL's random numbers are called 'pseudo-random'
  because rand() will generate the same series of
  "random" numbers if the seed is the same
• Getting the same series of random numbers can be
  useful for code testing
• It can also be very dangerous when used for other
  purposes (generating random passwords)

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Randomization

• How to get a good seed?
• The default seed is time()
• If you do not explicitly call the srand()
  function, then PERL will call it for you the
  first time you use rand().
• PERL uses srand(time) and this is good enough for
  our purposes

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Randomization

• calling the rand function without an argument
  generates random numbers from 0 to 1
• example
• x rand()
• print "x x \n"
• output x 0.348843242566318

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Randomization

• calling the rand function with an argument
  generates random numbers from 0 to N
• example
• x rand(10)
• print "x x \n"
• output x 6.2584777484949

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Randomization

• if you want random integers, use the int()
  function
• example
• x int rand(10)
• print "x x \n"
• output x 4

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Randomization

• if you want a random element from an array, call
  the rand function using _at_list as the argument
• in a "scalar context", _at_list returns the number
  of elements in the array
• example
• _at_list qw(dog cat fish)
• index int rand(_at_list)
• print "random listindex \n"
• output random cat

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Randomization

• if you want a random element from an array, call
  the rand function using _at_list as the argument
• example
• _at_list qw(dog cat fish)
• print "random listrand _at_list \n"
• output random fish
• Note this works without int()

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Randomization

• array indices do NOT have to be integers!
• list2.18171635 same as list2
• examples
• list2.9988494 same as list2
• list2.1086304 same as list2
• list0.9988494 same as list0
• PERL expects array indices to be integers
• When it finds decimal numbers, it truncates
• NOTE truncate ? round
• int() also truncates

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Coin Toss Simulator

• Random numbers are great for simulations
• If you flip a coin 4 times, how often will you
  get 4 heads? gt 0.54 0.0625
• Test this with PERL
• flip_coin 4 times gt count if you get 4 heads
• repeat many times gt report

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Sequence Scrambler

• Patterns occur in protein sequences
• How can you tell if patterns are random?
• A common test is to "scramble" a protein sequence
  and compare the native sequence to the scramble.
  
• The scramble should have the same number of amino
  acids, the same molecular weight, pI and other
  properties. Only the order of the amino acids is
  changed.

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Sequence Scrambler

• my _at_aas split(//, input)
• while(_at_aas)
• my index int rand _at_aas
• scramble. aasindex select
  random aa
• splice(_at_aas, index, 1) remove
  selection
• return scramble

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Sequence Scrambler

• Splice function allows you to take elements out
  of an array and/or replace them with other
  elements

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Sequence Scrambler

• Splice function allows you to take elements out
  of an array and/or replace them with other
  elements
• splice(_at_aas, index, 1)
• removes 1 element from array _at_aas gt aasindex
• splice(_at_aas, index, 3)
• removes 3 elements from array _at_aas
• aasindex, aasindex1, aasindex2

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Sequence Scrambler

• Splice function allows you to take elements out
  of an array and/or replace them with other
  elements
• splice(_at_aas, index, 1, 'A')
• exchanges 1 element from array _at_aas
• aasindex now contains 'A'
• splice(_at_aas, index, 3, ('A', 'G', 'C', 'T'))
  
• exchanges 3 elements from array _at_aas and inserts
  4

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Sequence Scrambler

• Splice function allows you to take elements out
  of an array and/or replace them with other
  elements