An Introduction to Perl Part 2

1. An Introduction to PerlPart 2 CSC8304 – Computing Environments for Bioinformatics - Lecture 8

2. Objectives • To introduce the Perl programming language • Lists, arrays, hashes • Recommended Books: • SAMS – Teach yourself Perl in 24 hours – Clinton Pierce • Beginning Perl for Bioinformatics – James Tisdall • The Best way to learn Perl is to read the books, numerous tutorials and to Practice. • These notes are not a comprehensive tutorial – reading extra material is essential CSC8304 – Computing Environments for Bioinformatics - Lecture 8

3. Lists • A list is an ordered collection of scalars. • Space for lists is dynamically allocated and removed from the program's memory as required • Parenthesis () are used to construct the list. Commas separate elements, • Creates a four element list containing the numbers 5, the word apple, the contents of the scalar variable $x and pi. • If the list contains only simple strings then can use the qw (quote) operator to avoid many quotation marks • (5, ‘apple’, $x, 3.14159) • qw (5 apple $x 3.14159) CSC8304 – Computing Environments for Bioinformatics - Lecture 8

4. Arrays • Literal lists are usually used to initialise some other structure • In Perl this can be an array or a hash • To create an array in Perl you just put something into it • Unlike Java, you don’t have to initialise it to a specific size before hand • This is an array assignment using the = sign as array assignment operator • Array assignments can involve other arrays or empty lists e.g. • @boys= qw(Greg Peter Bobby Quentin); • @copy=@original; • @clean=(); CSC8304 – Computing Environments for Bioinformatics - Lecture 8

5. Getting elements from Arrays • Elements in an array can be searched, values changed, or individual elements removed. • The simplest way to get the contents out of the entire array is to use the array in double quotation marks: • Prints the elements of @array with a space separating each element • Individual elements in an array are accessed by an index, as shown in the following code. • As in Java, the index starts at 0 and increases by 1 for each additional element. • To access an element use the syntax • Where array is the array name and index is the index of the element you want • print “@array”; • $array[index]; CSC8304 – Computing Environments for Bioinformatics - Lecture 8

6. Some example of using Arrays • Notice that individual elements of the array are referred to using a $ • This is because it refers to a single scalar value within the array • Finding the size of the array: • @trees=qw(oak cedar maple apple); • print $trees[0]; #prints “oak”; • print $trees[3]; #prints “apple”; • $trees[4]=‘pine’; • $size=@array; CSC8304 – Computing Environments for Bioinformatics - Lecture 8

7. Stepping through an array • This is one way to step through the array • An easier way in Perl… • @flavours=qw(choc vanilla strawberry mint sherbet); • for($index=0; $index<@flavours; $index++) • { • print “My favourite is $flavours[$index] and ..”; • } • print “many others.\n”; • foreach $cone (@flavours) • { • print “I’d like a $cone ice cream please \n”; • } • Last element of an array: • $#arrayname – e.g. print $#flavours; prints ‘sherbet’ CSC8304 – Computing Environments for Bioinformatics - Lecture 8

8. Converting scalars to arrays • Perl provides a number of functions and operators for converting between these two types • One method is to use the split function to convert a scalar into an array. • Split takes a pattern and a scalar and uses the pattern to split apart the scalar • The first argument is the pattern, the second the scalar to split e.g. • @words now contains each of the words the, slow, brown, fox without the spaces • If you don’t specify a string the variable $_ is used – one of Perls special reserved variable • If you don’t specify a pattern or string whitespace is used to split apart the variable $_ • @words=split(/ /,”the slow brown fox”); CSC8304 – Computing Environments for Bioinformatics - Lecture 8

9. Converting scalars to arrays • The patterns used by split are called regular expressions. • Regular expressions are a pattern matching language that we will discuss a bit later CSC8304 – Computing Environments for Bioinformatics - Lecture 8

10. Hashes • Hashes are another kind of collective data type • Like arrays, hashes contain a number of scalars • The difference is hashes access their scalar data by name, not by a numeric subscript like arrays do • Hash elements have two parts: • A key – identifies each element of the hash • A value – the data associated with that key • This relationship is called a key-value pair • A hash in Perl can contain as many elements as available memory will allow. Hashes are re-sized as elements are added and deleted. • Access to elements in a hash is extremely fast CSC8304 – Computing Environments for Bioinformatics - Lecture 8

11. Hashes • Example of when we might use a hash: • If we wanted to store information on licensed drivers, we might use the driver’s license number as the key • This is unique per driver • The data associated with each license number, the value, would be the driver’s information (license type, addess, age, etc) • Each driver’s license would represent an element in the hash • The (license, information) would be the key-value pair • To search for a particular entry, we look for the unique key first, which is very fast CSC8304 – Computing Environments for Bioinformatics - Lecture 8

12. Hashes – Putting data in • Hash variables in Perl are indicated by the percent sign (%). Individual elements are accessed using the $ just as with Arrays. • Individual hash elements are created by assigning values to them: • This assignment creates a relationship in the hash between Dune and Frank Herbert. The value associated with the key, $Authors(‘Dune’),can be treated like any other scalar • %Authors; • $Authors(‘Dune’)=‘Frank Herbert’; The value Frank Herbert The key Dune The hash %Authors CSC8304 – Computing Environments for Bioinformatics - Lecture 8

13. Hashes – Putting data in • To put several values into a hash, you could use a series of assignments from key to value: • Or, you could use a shortcut, listing pairings of keys and values: • Or, to help keep track of keys and values, use the => operator: • To be completely lazy, the left hand side of the => operator is expected to be a string, so need not even be quoted. • $food(‘apple’)=‘fruit’; • $food(‘pear’)=‘fruit’; • $food(‘carrot’)=‘vegetable’; • %food = (‘apple’, ‘fruit’, ‘pear’, ‘fruit’, ‘carrot’, ‘vegetable’); • %food = (‘apple’ => ‘fruit’, • ‘pear’ => ‘fruit’, • ‘carrot’ => ‘vegetable’); CSC8304 – Computing Environments for Bioinformatics - Lecture 8

14. Hashes – Getting data out • As we have seen, we can retrieve single elements of a hash with a $: • To access all elements of a hash: • %movies = (‘The Shining’ => ‘Kubrick’, • ‘Alien’ => ‘Scott’, • ‘Kill Bill’ => ‘Tarantino’); • print $movies(‘The Shining’); • foreach $film (keys %movies) • { • print “$film was directed by $movies{$film}.\n”; • } $movies{film} retrieves the element of the hash represented by the key $film contains the value of a hash key CSC8304 – Computing Environments for Bioinformatics - Lecture 8

15. Hashes – Getting data out • Perl also provides the values function to retrieve all the values stored in a hash. The values are returned in the same order as the keys function would return the keys: • In the example above, the name of the director contained in $Directors[0] corresponds to the name of the movie stored in $Films[0] and so on • It is possible to invert a hash, where all the keys of the original hash become values, and all the values of the original hash become keys: • @Directors = values %movies; • @Films = keys %movies; • %movies = (‘The Shining’ => ‘Kubrick’, • ‘Alien’ => ‘Scott’, • ‘Kill Bill’ => ‘Tarantino’); • %byDirector = reverse %movies; CSC8304 – Computing Environments for Bioinformatics - Lecture 8

16. Hashes and Lists and Arrays • Whenever a hash is used in a list context, Perl unwinds the hash back into a flat list of keys and values. This list can be assigned to an array, just like any other list: • In the example above, @data is an array containing six elements. The even elements are the keys, and the odd elements the values. You can perform any operation you require on the array @data, and then reassign the contents to %movies: • You can also copy and combine hashes (beware that keys need to be unique): • %movies = (‘The Shining’ => ‘Kubrick’, • ‘Alien’ => ‘Scott’, • ‘Kill Bill’ => ‘Tarantino’); • @data = %movies; • %movies = @data; • %new_hash = %old_hash; #copying a hash • %both = (%first, %second); #combining two hashes • %additional = (%both, key1 => ‘value1’, key2 => ‘value2’); • #adding two more key-value pairs CSC8304 – Computing Environments for Bioinformatics - Lecture 8

17. Hashes – Special operations • To test whether a key exists in a hash, use the exists function: • To remove a key from a hash, use the delete function: • To remove all the keys and values from a hash, simply reinitialise the hash to an empty list like this: • The keys function returns a list of all the keys in the hash, and we can use the sort function to order that list: • if ( exists $myHash{keyval} ) • { • #etc • } • delete $myHash{keyval}; • %myHash = (); • foreach ( sort keys %words ) • { • print “$_ $words{$_}\n”; • } CSC8304 – Computing Environments for Bioinformatics - Lecture 8

18. Useful things to do with Hashes • Many of the interesting things to do with hashes involve array manipulation • See the literature for more examples • One quick example is how to find the unique elements in an array: initialise a temporary hash %seen • %seen = (); • foreach (@wordsArray) • { • $seen{$_} = 1; • } • @uniquewords = keys %seen; • print “@uniquewords”; iterate over the array @wordsArray, setting $_ to each word in turn create an entry in the hash with the key $_ for each entry not already seen, with dummy value 1. print out the contents of @uniquewords extract all keys from the hash into the array @uniquewords CSC8304 – Computing Environments for Bioinformatics - Lecture 8

19. Summary • Lists • Arrays • Conversion of scalars to arrays using patterns • Hashes • Conversions between hashes, arrays and lists CSC8304 – Computing Environments for Bioinformatics - Lecture 8

20. Q & A – 1 • Are these lists equivalent: (5, ‘apple’, $x, 3.14159) and qw (5 apple $x 3.14159) ? • What will be the contents of the array: @clean=(); ? • If @trees=qw(oak cedar maple apple); is it correct to refer to the third element of the array as @trees[3] ? • What will be the value of $size=@trees ? • What will be the values of $tree in the following context foreach $tree (@trees) { print “Select the $tree tree \n”; } CSC8304 – Computing Environments for Bioinformatics - Lecture 8

21. Q & A – 2 • Is it true that $@arrayname gets the last element of the array arrayname ? • What will be the contents of the array words @words=split(/ /,”the slow brown fox”); ? • Do we need a key for each value in a hash ? • Is it correct to create hash as follows: %food = (‘apple’ => fruit, ‘pear’ => fruit, ‘carrot’ => vegetable); ? CSC8304 – Computing Environments for Bioinformatics - Lecture 8

22. Q & A – 3 • Can we invert a hash by using the ‘reverse’ operator ? Does this change keys into values and values into keys ? • What will be result of %both = (%first, %second); if %first and %second are hashes ? • Is it allowed to do @data = %movies; then perform operations on the @data array and then do %movies = @data; ? • Is it true that delete $myHash{keyval}; and %myHash = (); are equivalent ? CSC8304 – Computing Environments for Bioinformatics - Lecture 8