Term
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Definition
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Term
| what is the binding operator |
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Definition
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Term
| what does the binding operator mean |
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Definition
| apply the operation on the right to the string on the left |
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Term
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Definition
| variable that stores multiple scalars |
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Term
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Definition
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Term
| test for numerical equality |
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Definition
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Term
| what should you always do with systems calls |
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Definition
| check for failure e.g. when trying to open a file, always check that the filename exists using unless loop |
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Term
what does this mean
/^\s*$/ |
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Definition
regular expression //
^ from the beginning of the string
\s : whitespace, tab, newline, formfeed
* is zero or more times there
$ to the end of the string |
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Term
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Definition
| $& the string matched by the last successful pattern match |
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Term
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Definition
$sequence =~ /$motif/
**This returns a boolean**
the result is given by $& |
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Term
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Definition
| $A = ($sequence =~ tr/Aa//); |
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Term
| count A's in sequence using a while loop |
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Definition
while ($sequence =~ /a/ig) {
$A++;
}
** i means case insensitive
++ g means global - i.e. stop when you get to end of sequence |
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Term
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Definition
| within a subroutine the array @_ contains the parameters that were passed to the subroutine |
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Term
| naming your arguments in a subroutin |
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Definition
| my($dna, $protein, $gene_name) = @_; |
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Term
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Definition
| is the name of the program in question |
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Term
| # read in the DNA from the command line |
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Definition
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Term
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Definition
| contains the command line arguments intended for the script |
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Term
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Definition
| first argument from command line arguments NOT the programs name |
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Term
| subroutine with multiple arguments |
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Definition
sub routine() {
my($scalar, $array, $hash) = @_;
$$scalar++;
join(@$array);
join(%$hash);
return blah;
}
** NB changes to arguments in subroutine are carried into main routine |
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Term
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Definition
| routine(\$scalar, \@array, \%hash); |
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Term
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Definition
@LIST = grep(EXPRESSION, @ARRAY);
Perl's grep() function runs a regular expression on each element of an array, and returns only the elements that evaluate to true.
@myNames = ('Jacob', 'Michael', 'Joshua', 'Matthew', 'Alexander', 'Andrew');
@grepNames = grep(!/^A/, @myNames);
In the above example, the regular expression is looking for any value that does not start with a capital A. After sifting through the contents of the @myNames array, the value of @grepNames becomes ('Jacob', 'Michael', 'Joshua', 'Matthew'). |
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Term
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Definition
$ice="cold";
$length_ice = length ($ice); |
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Term
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Definition
| $portion = substr($string_variable, start number, length); |
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Term
| three things to remember about modules |
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Definition
1. suffix is .pm
2. when they are CALLED the suffix is not used: use BegPerlBioinformatics
3. the last line in the module must be 1; |
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Term
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Definition
| my @array = ('a','b','c'); |
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Term
| seed a random number generator |
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Definition
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Term
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Definition
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Term
| give the number of elements in an array |
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Definition
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Term
| remove the fractional part of the number $number |
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Definition
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Term
| return a random number greater than 0 and less than $number |
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Definition
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Term
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Definition
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Term
| a popular way to pick a perl seed |
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Definition
time|$$
(combining the time and the ID of the perl programme that is currently running |
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Definition
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Term
| specific element if an array |
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Definition
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Term
| code for random element in an array |
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Definition
| $array[int rand scalar @array] |
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Term
| really fast code for random element in an array |
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Definition
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Term
| what do you need to remember before calling rand |
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Definition
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Term
| random position in a string |
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Definition
int(rand(length($string)))
which is the same as
int rand length $string |
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Term
| in a string replace char at position $position with $newchar |
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Definition
| substr($string, $position, 1, $newchar); |
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Term
| initialise an empty array |
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Definition
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Term
| what does the push function do |
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Definition
Perl's push() function is used to push a value or values onto the end of an array, which increases the number of elements. The new values then become the last elements in the array.
push(@array,$string) |
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Term
| turn a decimal into a percent |
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Definition
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Term
| how to select all combinations of two elements from a set: |
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Definition
Nested loop:
for (my $i=0; $i<10; $i++) {
for (my $j = $i+1; $j<10; $j++) {
}
} |
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