Perl: arrays

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Perl arrays
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• !/usr/bin/perl -w
• bind3.pl
• Here's an example that takes a unix path
  (file)
• and copies it to anothe variable (filename)
• Then, we search for one or more of any
  character .
• followed by a "/" character -- but we have to
  use the
• escape metacharacter "\" so that we don't end
  the match \/.
• Finally, we are looking for one or more
  non-white spaces (\S)
• at the end -- to pull off the the last file
  name "FOUND"
• path "/home/tabraun/test/bob/FOUND"
• filename path
• filename s/.\/(\S)/1/
• print "filename\n"

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!/usr/bin/perl randomSeq.pl Don't get too
uptight over this line -- it is just setting a
"seed" for the rand() fuction with a value that
approximates a random number. If you must
know, it takes a prccess ID (), shifts its
bit left 15 times, then add the process ID to the
shifted value, then does an bit-wise XOR ()
with the current time(). print "Enter length
of sequence to generate" length
ltSTDINgt srand(time() ( ( ltlt 15))
) while(length) stay in loop until have
generated enough sequence rand int rand(4)
Interger number between (0-3) inclusive rand
tr/0123/ACTG/ length length-1
decrease loop counter seq seq . rand
keep the nucleotide I just created Since I
am out of the loop, I must be done print
"seq\n"
4

• Run Example
• Show process ID

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Lists and Arrays

• list ordered collection of scalars
• array a perl variable that contains a list
• each element of an array is a separate scalar
  variable
• values are ordered, from the first to the last
• elements are indexed by small integers, starting
  at 0

"left-most"
0 1 2 3 4 5
35
12.4
"hello, world"
indices
1.72e30
"bye\n"
69
"right-most"
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Accessing Elements of an Array

• fred0 "yabba"
• fred1 "dabba"
• fred2 "doo"
• fred3 4
• fred3
• fred1 s/b/B/g
• fred 32 completely different scalar

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Creating Elements

• if you store into an array element that is beyond
  the end of the array, the array is automatically
  extended as needed (no limit as long as there is
  memory available)
• intervening elements will be undef
• rocks0 'bedrock'
• rocks1 'slate'
• rocks99 'chasm' 3 defined elements, 97
  undef
• .

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List Literals

• shorthand for creating arrays
• (1,2,3) list of 3 values, 1, 2, 3
• (1, 2, 3,) same thing, last comma ignored
• ("fred",4.5) 2 values
• () empty list
• (1..100) list of integers, 1 thru 100
• aka "range operator"
• (1..5) 1, 2, 3, 4, 5
• (5..1) empty, only counts up
• (0, 2..6, 10) (0, 2, 3, 4, 5, 6, 10)
• (a..b) depends on a and b

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Another List Shortcut

• qw -- stands for "quoted words"
• ("fred", "barney", "betty", "wilma", "dino")
• same as
• qw/ fred barney betty wilma dino /
• same as above with less typing

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List Assignment

• list values may be assigned to variables
• (fred, barney, dino) ("finstone", "rubble",
  undef)
• can use to swap
• (fred, barney) (barney, fred)
• Note you cannot do this in most other
  languages (C, Java, etc)
• Extra right side values are ignored
• Extra left side variables will be undef
• (fred, barney) qw/ flintstone rubble slate /
  slate ignored
• (wilma, dino) qw/flintstone/ dino gets
  undef

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List Assignment

• can build array
• (r0, r1, r2) qw/ slate granite chalk/
• one final array shortcut -- _at_
• _at_rocks qw/ bedrock slate lava/
• rocks2 s/s/S/
• _at_empty_array ()
• _at_list (1..10) 10 elements of 1-10
• _at_stuff (_at_list, _at_rocks) 13 elements
• dino "dog"
• _at_quarry (_at_rocs, "diamond", _at_list, dino)
• Array names are replaced by the elements in its
  list

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Copying an Array is Easy

• _at_copy _at_quarry all elements are copied
• for(I0IltnumI)
• copyI quarryI

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Array Manipulations

• could add to arrays by storing them into elements
  with new, larger indices
• however, this defeats the strengths of perl, and
  will actually result in slower code
• extensive use of indices slows down perl

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Array as a Stack

• elements are added/removed from the "right" side
  of the list (portion with highest indices)
• Syntax
• push ARRAY, LIST
• - returns new number of elements in array
• pop ARRAY
• - returns right most element of array/list
• _at_array (5..9) array has
  5,6,7,8,9
• fred pop(_at_array) fred 9, array
  5,6,7,8
• barney pop _at_array barney 8, array 5,6,7
• pop _at_array 7 is discarded,
  array 5, 6

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• push (_at_array, 0)
• push _at_array, 8
• _at_list (5, 6, 7)
• push (_at_array, _at_list)

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An Array as a Queue

• Elements are added/removed from the left (or
  portion with lowest indices)
• shift ARRAY
• - returns left most element
• unshift ARRAY, list
• - returns new number of elements in array
• _at_array qw/ dino fred barn /
• a shift(_at_array) _at_array fred, barn
• b shift _at_array _at_array barn
• shift _at_array _at_array is empty
• c shift _at_array _at_array still empty, c
  undef
• unshift(_at_array,5) _at_array now has 5
• _at_list (1..4)
• unshift(_at_array,_at_list) _at_array 1,2,3,4,5

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Mix and Match

• _at_array (9..13)
• push(_at_array, 14)
• unshift(_at_array,8)
• fourteen pop(_at_array)
• nine shift _at_array
• print "array2"

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Interpolating into Arrays

• Like scalars, array values my be interpolated
  into double-quoted strings
• _at_rocks qw/ stone gravel rubble /
• print "boulder _at_rocks marble\n" inserts spaces
  between elements of array
• print "rocks1\n" gravel

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Foreach loop revisited

• foreach SCALAR (ARRAY)
• -- steps through each item of an array executing
  one iteration each time thru the loop
• _at_rocks qw /bedrock pebbles stone/
• foreach rock (_at_rocks)
• print "One rock is rock\n"

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Control Loop Variable

• A change to the control loop variable actually
  changes the elements of the array.
• rock "Haggar" rock is stored and saved by
  perl
• _at_rocks qw/ slate stone marble /
• foreach rock (_at_rocks)
• rock s/(.)/\U1/
• print "_at_rocks\n" SLATE STONE MARBLE
• print "rock\n" Haggar restored ???

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Other Array Operators

• reverse ARRAY
• -- takes an array of items and reverses the
  order
• _at_fred 5..10
• _at_derf reverse (_at_fred) 10 9 8 7 6 5
• _at_fred reverse _at_fred fred is now reversed too
• reverse SCALAR
• -- in a scalar context, such as the string
  ATGCC, reverse will reverse the order of the
  string -- CCGTA

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Other Array Operators

• sort ARRAY
• -- takes a list of values and sorts them in
  character order (lexigraphically)
• _at_rocks qw/ slate stone marble /
• _at_nums (97, 98, 99 100, 101)
• _at_sorted sort (_at_rocks) marble slate stone
• _at_nums sorted (_at_nums) 100 101 97 98 99

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Array-like Operator

• glob EXPR
• -- In list context, returns a (possibly empty)
  list of filename expansions on the value of EXPR
  such as the standard Unix shell /bin/csh would do
• Ex)
• _at_files glob ''

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Examples

• Multiple syntax for arrays

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End
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Other topics

• sort
• reverse
• glob
• split
• system and
• array growth/memory allocation
• pop, push, shift, unshift
• slice
• building 2-d arrays
• arrays of hashes and hashes of arrays
• Other
• _at_ARGV (modules, and module for long)
• file tests
• files and directories
• cgi-bin
• advanced sorting
• strings

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Side Note

• More on arrays in later lecture, however,
  question of arrays of arrays

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• !/usr/bin/perl
• _at_first (1,2,3,4,5)
• _at_second (10,20,30,40,50)
• _at_third (100,200,300,400,500)
• \_at_ is a "reference"
• _at_numbers (\_at_first,\_at_second,\_at_third)
• foreach i (_at_numbers) i becomes a reference
  to an array
• foreach j (_at_i) _at_ dereferences i (an
  reference to an aray)
• so j is an elemetn of
  an array
• print "j is value in arrayArray\n"
• print "\n"

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• ./arrayArray.pl
• 1 is value in arrayArray
• 2 is value in arrayArray
• 3 is value in arrayArray
• 4 is value in arrayArray
• 5 is value in arrayArray
• 10 is value in arrayArray
• 20 is value in arrayArray
• 30 is value in arrayArray
• 40 is value in arrayArray
• 50 is value in arrayArray
• 100 is value in arrayArray
• 200 is value in arrayArray
• 300 is value in arrayArray
• 400 is value in arrayArray
• 500 is value in arrayArray
• 400

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End
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Example

• Negative numbers in the sample source code I
  provided, I use the following REGEXP \d to
  verify that a "number" was entered.
• Note that this will not match a negative number
  (as in the example I ran during class) because it
  does not include a "-"
• Note, you should only set the seed ONCE doing
  so more often would actually decrease the
  approximation of a random number
• srand (time() ( ( ltlt 15)) )
• Examples
• What is "random" how would you verify that your
  output is random?
• You would expect each letter to occur about 25
  of the time.
• ./randSeq.pl gt look
• cat look grep A wc
• OR
• count the letters as you generate them and print