Data structure
Scalar
Creation:
$age = 25; # numeric
$name = "runoob"; # string
$string = 'This is
a multiline
string'; #multiline string
Operations: Context is everywhere in perl
$str = "hello" . "world"; # Concatenates strings.
$num = 5 + 10; # adds two numbers.
$mstr = $str * $num #$num repeats of $str
Escape Character:
\n, \\, \t ...
Array
Creation
@ages = (25, 30, 40);
@names = ("google", "runoob", "taobao");
Accessing elements
print "$ages[1]\n";
print "$ages[2]\n";
print "$names[0]\n";
print "$names[1]\n";
print "$ages[-1]\n";#Selecting from the end
Array Size
$size = @array;
Adding and removing elements
@coins = ("Quarter","Dime","Nickel");
push(@coins, "Penny");
pop(@coins);
shift(@coins);
unshift(@coins, "Dollar");
Slicing
@days = qw/Mon Tue Wed Thu Fri Sat Sun/;
@weekdays = @days[3..5];
replacing Array Element
@nums = (1..20);
@num[3] = 99
splice(@nums, 5, 4, 21..24);
Transform String to Arrays
$var_string = "Rain-Drops-On-Roses-And-Whiskers-On-Kittens";
@string = split('-', $var_string);
Transform Arrays to String
$string1 = join( '-', @string );
Sorting Array
@foods = qw(pizza steak chicken burgers);
@foods = sort(@foods);
Hash
Creating Hashes
%data = ('John Paul' => 45, 'Lisa' => 30, 'Kumar' => 40);
$data{'Lisa'} = 30;
$data{'Kumar'} = 40;
Accessing Hash Elements
print "$data{'Lisa'}\n";
Extracting Keys and Values
@names = keys %data;
@ages = values %data;
Checking for Existence
if( exists($data{'Lisa'}) ){
print "Lisa is $data{'Lisa'} years old\n";
}
Getting Hash Size
$size = @name;
Delet elements
delete $data{'Lisa'};
Multi-layer hash
open (TAXONOMY, "rankedlineage.dmp") or die "Can't open input: $!\n";
open (HOMOLOGY, "nonphage.genomic.unique-blastn-all-3-virus-hits-complete-sortByVirusThenByHit-head" . ".txt") or die "Can't open input: $!\n";
open (OUT, ">Homology-prediction" . ".tsv") or die "Can't open input: $!\n";
while ($line = readline(TAXONOMY)) {
chomp $line;
@info = split /\|/, $line;
# ///
s{^\s+|\s+$}{}g foreach @info;
$domain = $info[9];
$kingdom = $info[8];
$name = $info[1];
$taxid = $info[0];
$hash_taxonomy{$taxid}{name} = $name;
$hash_taxonomy{$taxid}{domain} = $domain;
}
while ($line = readline(HOMOLOGY)) {
chomp $line;
@info = split /\t/, $line;
$virus_id = $info[1];
$virus_name=$info[2];
$hit_id = $info[6];
$hit_name = $info[7];
$score = $info[5];
$hash{$virus_id}{$hit_id}{hit_name} = $hit_name;
$hash{$virus_id}{$hit_id}{score_sum} = $score;
$hash{$virus_id}{$hit_id}{domain} = $hash_taxonomy{$hit_id}{domain};
$hash_virus{$virus_id}{name} = $virus_name;
if (($virus_id eq $virus_id_pre) and ($hit_id eq $hit_id_pre)) {
$hash{$virus_id}{$hit_id}{score_sum} += $score;
} else {
$hash{$virus_id}{$hit_id}{score_sum} = $score;
}
$virus_id_pre = $virus_id;
$hit_id_pre = $hit_id;
}
foreach $virus (sort keys %hash) {
foreach $tax (@domain_uniq) {
foreach $host (sort keys %{$hash{$virus}}) {
if ($hash{$virus}{$host}{domain} eq $tax) {
$prediction{$virus}{domain}{$tax}{score} += $hash{$virus}{$host}{score_sum};
}
}
}
}
foreach $virus (sort keys %hash) {
print OUT "$hash_virus{$virus}{name}:"."$virus\t";
foreach $tax (sort {$prediction{$virus}{domain}{$b}{score} <=> $prediction{$virus}{domain}{$a}{score}} keys %{$prediction{$virus}{domain}}) {
print OUT "$tax:"."$prediction{$virus}{domain}{$tax}{score}\|";
}
print OUT "\n";
}
close HOMOLOGY;
close TAXONOMY;
close OUT;
Control flow
Conditional statement
$a = 2
print "It's positive\n" if $a > 0;
print "It's positive" unless $a < 0;
$status = ($a >0) ? "It's positive" : "It's nagative";
Loops: Similar to all other languages
for ( init; condition; increment ){
statement(s);
}
for( $a = 0; $a < 10; $a = $a + 1 ){
print "$a\n";
}
while( $a < 20 ){
printf "$a\n";
$a = $a + 1;
}
FILE IO
open(DATA1, "<file.txt") or die "file.txt can't be open, $!";
open(DATA2, ">file.txt") or die "file.txt can't be open, $!";
while ($line = readline(DATA1)) {
print DATA2 $line;
}
close DATA
