Transcript Perl: arrays

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 ($$),
# shifts its bit left 15 times, then add the process ID to the shifted
# value, then does an bit-wise XOR (^) with the current time().
#
print "Enter length of sequence to generate:";
$length = <STDIN>;
srand(time() ^ ($$ + ($$ << 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";
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• Run Example
• Show process ID
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Lists and Arrays
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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"
indices
0
35
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12.4
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"hello, world"
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1.72e30
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"bye\n"
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"right-most"
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Accessing Elements of an Array
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$fred[0] = "yabba";
$fred[1] = "dabba";
$fred[2] = "doo";
$fred[3] = 4;
$fred[3]++;
$fred[1] =~ 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
• $rocks[0] = 'bedrock';
• $rocks[1] = 'slate';
• $rocks[99] = '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
($r[0], $r[1], $r[2]) = qw/ slate granite chalk/;
• one final array shortcut -- @
@rocks = qw/ bedrock slate lava/;
$rocks[2] =~ s/s/S/;
@empty_array = ();
@list = (1..10); # 10 elements of 1-10
@stuff = (@list, @rocks); #13 elements
$dino = "dog";
@quarry = (@rocs, "diamond", @list, $dino);
• Array names are replaced by the elements in its list
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Copying an Array is Easy
@copy = @quarry; # all elements are copied
for($I=0;$I<$num;$I++)
{
$copy[$I] = $quarry[$I];
}
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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
@array = (5..9);
# array has 5,6,7,8,9
$fred = pop(@array);
# fred = 9, array = 5,6,7,8
$barney = pop @array; #barney = 8, array = 5,6,7
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pop @array;
# 7 is discarded, array = 5, 6
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push (@array, 0);
push @array, 8;
@list = (5, 6, 7);
push (@array, @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
@array = qw/ dino fred barn /;
$a = shift(@array); # @array = fred, barn
$b = shift @array; # @array = barn
shift @array; # @array is empty
$c = shift @array; # @array still empty, $c = undef
unshift(@array,5); #@array now has 5
@list = (1..4);
unshift(@array,@list); # @array = 1,2,3,4,5
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Mix and Match
@array = (9..13);
push(@array, 14);
unshift(@array,8);
$fourteen = pop(@array);
$nine = shift @array;
print "$array[2]";
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Interpolating into Arrays
Like scalars, array values my be interpolated
into double-quoted strings
@rocks = qw/ stone gravel rubble /;
print "boulder @rocks marble\n"; #inserts
spaces between elements of array
print "$rocks[1]\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
@rocks = qw /bedrock pebbles stone/;
foreach $rock (@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
@rocks = qw/ slate stone marble /;
foreach $rock (@rocks) {
$rock =~ s/(.*)/\U$1/;
}
print "@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
@fred = 5..10;
@derf = reverse (@fred); 10 9 8 7 6 5
@fred = reverse @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)
@rocks = qw/ slate stone marble /;
@nums = (97, 98, 99 100, 101);
@sorted = sort (@rocks); #marble slate stone
@nums = sorted (@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)
@files = glob '*';
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Examples
• Multiple syntax for arrays
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End
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Other topics
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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
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@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
@first = (1,2,3,4,5);
@second = (10,20,30,40,50);
@third = (100,200,300,400,500);
# \@ is a "reference"
@numbers = (\@first,\@second,\@third);
foreach $i (@numbers)
{
foreach $j (@$i)
{
print "$j is value
}
}
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i becomes a reference to an array
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@$ dereferences i (an reference to an aray)
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so j is an elemetn of an array
in arrayArray\n";
print "\n";
#### I much prefer this notation
print "$numbers[2][3]\n";
print "\n";
# and finally
for ($i = 0; $i < @numbers; $i++) {
$aref = $numbers[$i];
#so bizzare, my editor
for ($j = 0; $j <= $#{$aref}; $j++) {
#thinks this is comment
print "$numbers[$i][$j]\n"
# $#ARRAY returns index of last element
}
}
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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() ^ ($$ + ($$ << 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 > look
cat look | grep A | wc
OR
count the letters as you generate them and print
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