Joe Wood Environmental Genomics Thematic Programme Data Centre

Transcription

1 Getting started with Perl Joe Wood

2 Session content Writing a perl script Running a perl script Variables Scalars Arrays Hashes Using strict

3 Writing a perl script #!/usr/bin/perl -w Statements(;) Comments(#)

4 Writing a perl script gedit script1.pl #!/usr/bin/perl -w #print some text print Hello World\n ; Save

5 Running a perl script./script1.pl

6 Running a perl script./script1.pl Make your file executable (chmod u+x)!! chmod u+x script1.pl

7 Variables Variables are containers to hold values Values can change within a script Types Scalars single pieces of information Arrays lists of information Hashes 'look-up' table of information

8 Scalars Contain single pieces of info Naming conventions- Preceded by '$' No spaces (use '_') Usually lowercase e.g. $test_scalar Store various types including strings and numbers

9 Scalars Example./script2.pl $bit_of_text assigned value with '=' #!/usr/bin/perl -w #create variable with value of 'Hello World' $bit_of_text = Hello World\n ; print $bit_of text;

10 Scalars Example./script2.pl $bit_of_text assigned value with '=' Permissions! (chmod u+x) #!/usr/bin/perl -w #create variable with value of 'Hello World' $bit_of_text = Hello World\n ; print $bit_of text;

11 Simple arithmetic Script 3 #!usr/bin/perl -w $number1 = 2; $number2 = 3;

12 Simple arithmetic Script 3 #!usr/bin/perl -w $number1 = 2; $number2 = 3; $add = $number1 + $number2; print "Addition answer is $add\n";

13 Simple arithmetic Script 3 $subtract = $number2 - $number1; print "Subtraction answer is $subtract\n";

14 Simple arithmetic Script 3 $subtract = $number2 - $number1; print "Subtraction answer is $subtract\n"; $multiply = $number1 * $number2; print "Multiplication answer is $multiply\n";

15 Incrementing Numbers can be incremented with '++' $number1 = 3; $number1++; print $number1\n ;

16 Incrementing Numbers can be incremented with '++' $number1 = 3; $number1++; print $number1\n ; 4

17 Decrementing Numbers can be decremented with '--' $number1 = 3; $number1--; print $number1\n ;

18 Decrementing Numbers can be decremented with '--' $number1 = 3; $number1--; print $number1\n ; 2

19 Concatenation Strings can be concatenated with '.' $string1 = This ; $string2 = is ; $string3 = easy ; $string4 = so far ; print $string1.$string2.$string3.$string4;

20 Concatenation Strings can be concatenated with '.' $string1 = This ; $string2 = is ; $string3 = easy ; $string4 = so far ; print $string1.$string2.$string3.$string4; This is easy so far

21 Arrays List of information Each member of list is an element 8 hello 5.6 $something Preceded by '@'

22 Arrays Assign values using '=' and list = (8, hello,5.6,$something) 8 hello 5.6 $something

23 Arrays Assign values using '=' and list = (8, hello,5.6,$something) Refer to elements as: $test_array[element number] 8 hello 5.6 $something

24 Array Example 8 hello 5.6 $something $test_array[1] is

25 Array Example 8 hello 5.6 $something $test_array[1] is hello

26 Array Example 8 hello 5.6 $something $test_array[1] is hello arrays start at 0! $test_array[0] is 8

27 Arrays Take care with variable naming! $test_array[0] is unrelated to... $test_array

28 Array Functions pop remove from right hand side push add to right hand side shift remove from left hand side unshift add to left hand side

29 Script4 -pop and push POP into variable (variable=4) PUSH variable back onto array

30 Script4 -pop and push #create an = (8,54,78,2,5,6,4); #pop the last value $pop_test = pop (@an_array); #push $pop_test back on push (@an_array,$pop_test);

31 Script4 -shift and unshift SHIFT into variable (variable=8) UNSHIFT variable back onto array

32 Script4 -shift and unshift #shift the first value $shift_test = shift (@an_array); #unshift $shift_test back on unshift (@an_array,$shift_test);

33 Hashes Look-up table of 'Keys' with associated 'Values' e.g. Hash called 'car' KEY COLOUR SIZE SPEED VALUE BLUE BIG REALLY FAST

34 Hashes Keys are arbitrary scalars Preceded by %, e.g. %car Use keys to retrieve values: $test_hash{key}=value $car{colour}= blue

35 Script5 Hashes Example #Hash example - codon translation use strict; my %translate; $translate{'atg'} = 'M'; $translate{'taa'} = '*'; $translate{'ctt'} = 'L'; print "$translate{'atg'}\n";

36 Hash functions keys = keys(%translate) values = values(%translate)

37 Use strict 'use strict;' Forces you to declare variables before using them Good for when scripts get bigger Declarations start with 'my' e.g. my %translate;