The document discusses hashes in Perl. It explains that hashes store collections of scalars indexed by name like keys in a real-life phone directory. It provides examples of using hashes to store phone numbers and names, and accessing values using keys. It also discusses using foreach to iterate over hashes and sort to sort the keys or values of a hash.

1. Hashes and @ARGV Paolo Marcatili - Programmazione 08-09

2. Agenda Today we will see how to Summary of what we’ve done Hashes Keys Paolo Marcatili - Programmazione 08-09

3. Task Today Paolo Marcatili - Programmazione 08-09

4. parsing Parse a GO file Extract gene names and function Paolo Marcatili - Programmazione 08-09

5. Hashes Paolo Marcatili - Programmazione 08-09

6. Hashes Hashes are like array , they store collections of scalars ... but unlike arrays, indexing is by name (just like in real life!!!) Two components to each hash entry: Key example : name Value example : phone number Hashes denoted with % Example : %phoneDirectory Elements are accessed using {} (like [] in arrays) Paolo Marcatili - Programmazione 08-09

7. Hashes continued ... Adding a new key-value pair $phoneDirectory{“Shirly”} = 7267975 Note the $ to specify “scalar” context! Each key can have only one value $phoneDirectory{“Shirly”} = 7265797 # overwrites previous assignment Multiple keys can have the same value Accessing the value of a key $phoneNumber =$phoneDirectory{“Shirly”}; Paolo Marcatili - Programmazione 08-09

8. Hashes and Foreach Foreach works in hashes as well! foreach $person (keys (%phoneDirectory) ) { print “$person: $phoneDirectory{$person}”; } Never depend on the order you put key/values in the hash! Perl has its own magic to make hashes amazingly fast!! Paolo Marcatili - Programmazione 08-09

9. Hashes and Sorting The sort function works with hashes as well Sorting on the keys foreach $person ( sort keys %phoneDirectory) { print “$person : $directory{$person}\n”; } This will print the phoneDirectory hash table in alphabetical order based on the name of the person, i.e. the key. Paolo Marcatili - Programmazione 08-09

10. Hash and Sorting cont... Sorting by value foreach $person (sort {$phoneDirectory{$a} <=> $phoneDirectory{$b}} keys %phoneDirectory) { print “$person : $phoneDirectory{$person}\n”; } Prints the person and their phone number in the order of their respective phone numbers, i.e. the value. Paolo Marcatili - Programmazione 08-09

11. Exercise Chose your own test or use wget “ http://www.quirinale.it/costituzione/costituzione.htm ” Identify the 10 most frequent words Identify the 10 most frequent words longer than 5 letters Paolo Marcatili - Programmazione 08-09

12. Counting Words my %seen; while (my $l=<F>){ my @w=split (/\s+/, $l);# questa è una funzione nuova… foreach my $word (@w){ $word=~s/[sx]$//;#plurial elimination $seen { $word } ++; } } foreach my $word (sort {$seen{$a}<=>$seen{$b}} keys %seen){ print “Word $word N: $seen{$word}\n”; } Paolo Marcatili - Programmazione 08-09

13. @ARGV Paolo Marcatili - Programmazione 08-09

14. Command Line Arguments Command line arguments in Perl are extremely easy. @ARGV is the array that holds all arguments passed in from the command line. Example: % ./prog.pl arg1 arg2 arg3 @ARGV would contain ('arg1', arg2', 'arg3) $#ARGV returns the number of command line arguments that have been passed. Remember $#array is the size of the array! Paolo Marcatili - Programmazione 08-09

15. Quick Program with @ARGV Simple program called log.pl that takes in a number and prints the log base 2 of that number; #!/usr/local/bin/perl -w $log = log($ARGV[0]) / log(2); print “The log base 2 of $ARGV[0] is $log.\n”; Run the program as follows: % log.pl 8 This will return the following: The log base 2 of 8 is 3. Paolo Marcatili - Programmazione 08-09

16. $_ Perl default scalar value that is used when a variable is not explicitly specified. Can be used in For Loops File Handling Regular Expressions Paolo Marcatili - Programmazione 08-09

17. $_ and For Loops Example using $_ in a for loop @array = ( “Perl”, “C”, “Java” ); for(@array) { print $_ . “is a language I know\n”; } Output : Perl is a language I know. C is a language I know. Java is a language I know. Paolo Marcatili - Programmazione 08-09

18. $_ and File Handlers Example in using $_ when reading in a file; while( <> ) { chomp $_; # remove the newline char @array = split/ /, $_; # split the line on white space # and stores data in an array } Note: The line read in from the file is automatically store in the default scalar variable $_ Paolo Marcatili - Programmazione 08-09

19. Opendir, readdir Paolo Marcatili - Programmazione 08-09

20. Opendir & readdir Just like open, but for dirs # load all files of the &quot;data/&quot; folder into the @files array opendir(DIR, ”$ARGV[0]&quot;); @files = readdir(DIR); closedir(DIR); # build a unsorted list from the @files array: print &quot;<ul>&quot;; foreach $file (@files) { next if ($file eq &quot;.&quot; or $file eq &quot;..&quot;); print &quot;<li><a href=\&quot;$file\&quot;>$file</a></li>&quot;; } print &quot;</ul>&quot;; Paolo Marcatili - Programmazione 08-09

21. Task Paolo Marcatili - Programmazione 08-09

22. Malaria proteins annotations We’ll do a script that reports all gene with a similar function w.r.t. our query gene. http://www. biocomputing . it/master_hashes Paolo Marcatili - Programmazione 08-09