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Introduction to Perl

Part II

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Associative arrays or Hashes

Like arrays, but instead of numbers as indices can use strings

@array = (‘john’, ‘steve’, ‘aaron’, ‘max’, ‘juan’, ‘sue’)

%hash = ( ‘apple’ => 12, ‘pear’ => 3, ‘cherry’ =>30, ‘lemon’ => 2, ‘peach’ => 6, ‘kiwi’ => 3);

10 2 3 4 5

Array Hashpear

apple

cherry

lemon

peach

kiwi‘jo

hn

’

‘st

eve’

‘aaro

n’

‘m

ax’

‘ju

an

’

‘su

e’

123

30263

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Using hashes

{ } operator

Set a value– $hash{‘cherry’} = 10;

Access a value– print $hash{‘cherry’}, “\n”;

Remove an entry– delete $hash{‘cherry’};

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Get the Keys

keys function will return a list of the hash keys

@keys = keys %fruit;

for my $key ( keys %fruit ) { print “$key => $hash{$key}\n”;}

Would be ‘apple’, ‘pear’, ...

Order of keys is NOT guaranteed!

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Get just the values

@values = values %hash;

for my $val ( @values ) { print “val is $val\n”;}

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Iterate through a set

Order is not guaranteed!while( my ($key,$value) = each %hash){ print “$key => $value\n”;}

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Subroutines

Set of code that can be reused

Can also be referred to as procedures and functions

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Defining a subroutine

sub routine_name { }

Calling the routine– routine_name;

– &routine_name; (& is optional)

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Passing data to a subroutine

Pass in a list of data– &dosomething($var1,$var2);

– sub dosomething { my ($v1,$v2) = @_;}sub do2 { my $v1 = shift @_; my $v2 = shift;}

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Returning data from a subroutine

The last line of the routine set the return valuesub dothis { my $c = 10 + 20;}print dothis(), “\n”;

Can also use return specify return value and/or leave routine early

sub is_stopcodon { my $val = shift @_; if( length($val) != 3 ) { return -1; } elsif( $val eq ‘TAA’ || $val eq ‘TAG’ || $val eq ‘TGA’ ) { return 1; } else { return 0; }

Write subroutine which returns true if codon is a stop codon (for standard

genetic code).-1 on error, 1 on true, 0 on false

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Context

array versus scalar context my $length = @lst;

my ($first) = @lst;

Want array used to report context subroutines are called in

Can force scalar context with scalarmy $len = scalar @lst;

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subroutine context

sub dostuff { if( wantarray ) { print “array/list context\n”; } else { print “scalar context\n”; }}

dostuff(); # scalarmy @a = dostuff(); # arraymy %h = dostuff(); # arraymy $s = dostuff(); # scalar

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Why do you care about context?

sub dostuff { my @r = (10,20); return @r;}

my @a = dostuff(); # arraymy %h = dostuff(); # arraymy $s = dostuff(); # scalar

print “@a\n”; # 10 20print join(“ “, keys %h),”\n”; # 10print “$s\n”; # 2

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References

Are “pointers” the data object instead of object itsself

Allows us to have a shorthand to refer to something and pass it around

Must “dereference” something to get its actual value, the “reference” is just a location in memory

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Reference Operators

\ in front of variable to get its memory location– my $ptr = \@vals;

[ ] for arrays, { } for hashes

Can assign a pointer directly– my $ptr = [ (‘owlmonkey’, ‘lemur’)];

my $hashptr = { ‘chrom’ => ‘III’, ‘start’ => 23};

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Dereferencing

Need to cast reference back to datatype

my @list = @$ptr;

my %hash = %$hashref;

Can also use ‘{ }’ to clarify– my @list = @{$ptr};

– my %hash = %{$hashref};

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Really they are not so hard...

my @list = (‘fugu’, ‘human’, ‘worm’, ‘fly’);

my $list_ref = \@list;

my $list_ref_copy = [@list];

for my $item ( @$list_ref ) { print “$item\n”;}

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Why use references?

Simplify argument passing to subroutines

Allows updating of data without making multiple copies

What if we wanted to pass in 2 arrays to a subroutine?

sub func { my (@v1,@v2) = @_; }

How do we know when one stops and another starts?

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Why use references?

Passing in two arrays to intermix.sub func {

my ($v1,$v2) = @_; my @mixed; while( @$v1 || @$v2 ) { push @mixed, shift @$v1 if @$v1; push @mixed, shift @$v2 if @$v2; } return \@mixed;}

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References also allow Arrays of Arrays

my @lst;push @lst, [‘milk’, ‘butter’, ‘cheese’];push @lst, [‘wine’, ‘sherry’, ‘port’];push @lst, [‘bread’, ‘bagels’, ‘croissants’];

my @matrix = [ [1, 0, 0], [0, 1, 0], [0, 0, 1] ];

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Hashes of arrays

$hash{‘dogs’} = [‘beagle’, ‘shepherd’, ‘lab’];$hash{‘cats’} = [‘calico’, ‘tabby’, ‘siamese’];$hash{‘fish’} = [‘gold’,’beta’,’tuna’];

for my $key (keys %hash ) { print “$key => “, join(“\t”, @{$hash{$key}}), “\n”;}

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More matrix use

my @matrix;open(IN, $file) || die $!;# read in the matrixwhile(<IN>) { push @matrix, [split];}# data looks like# GENENAME EXPVALUE STATUS# sort by 2nd columnfor my $row ( sort { $a->[1] <=> $b->[1] } @matrix ) { print join(“\t”, @$row), “\n”;}

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Funny operators

my @bases = qw(C A G T)

my $msg = <<EOFThis is the message I wanted to tell you aboutEOF;

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Part of “amazing power” of Perl

Allow matching of patterns

Syntax can be tricky

Worth the effort to learn!

Regular Expressions

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if( $fruit eq ‘apple’ || $fruit eq ‘Apple’ || $fruit eq ‘pear’) { print “got a fruit $fruit\n”;}if( $fruit =~ /[Aa]pple|pear/ ){ print “matched fruit $fruit\n”;}

A simple regexp

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use the =~ operator to match

if( $var =~ /pattern/ ) {} - scalar context

my ($a,$b) = ( $var =~ /(\S+)\s+(\S+)/ );

if( $var !~ m// ) { } - true if pattern doesn’t

m/REGEXPHERE/ - match

s/REGEXP/REPLACE/ - substitute

tr/VALUES/NEWVALUES/ - translate

Regular Expression syntax

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Search a string for a pattern match

If no string is specified, will match $_

Pattern can contain variables which will be interpolated (and pattern recompiled)while( <DATA> ) { if( /A$num/ ) { $num++ }}while( <DATA> ) { if( /A$num/o ) { $num++ }}

m// operator (match)

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m// -if specify m, can replace / with anything e.g. m##, m[], m!!

/i - case insensitive

/g - global match (more than one)

/x - extended regexps (allows comments and whitespace)

/o - compile regexp once

Pattern extras

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\s - whitespace (tab,space,newline, etc)

\S - NOT whitespace

\d - numerics ([0-9])

\D - NOT numerics

\t, \n - tab, newline

. - anything

Shortcuts

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+ - 1 -> many (match 1,2,3,4,... instances )/a+/ will match ‘a’, ‘aa’, ‘aaaaa’

* - 0 -> many

? - 0 or 1

{N}, {M,N} - match exactly N, or M to N

[], [^] - anything in the brackets, anything but what is in the brackets

Regexp Operators

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Things in parentheses can be retrieved via variables $1, $2, $3, etc for 1st,2nd,3rd matches

if( /(\S+)\s+([\d\.\+\-]+)/) { print “$1 --> $2\n”;}

my ($name,$score) = ($var =~ /(\S+)\s+([\d\.\+\-]+)/);

Saving what you matched

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Simple Regexp

my $line = “aardvark”;if( $line =~ /aa/ ) { print “has double a\n” }if( $line =~ /(a{2})/ ) { print “has double a\n” }if( $line =~ /(a+)/ ) { print “has 1 or more a\n” }

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Matching gene names

# File contains lots of gene names# YFL001C YAR102W - yeast ORF names# let-1, unc-7 - worm names http://biosci.umn.edu/CGC/Nomenclature/nomenguid.htm# ENSG000000101 - human Ensembl gene nameswhile(<IN>) { if( /^(Y([A-P])(R|L)(\d{3})(W|C)(\-\w)?)/ ) { printf “yeast gene %s, chrom %d,%s arm, %d %s strand\n”, $1, (ord($2)-ord(‘A’))+1, $3, $4; } elsif( /^(ENSG\d+)/ ) { print “human gene $1\n” } elsif( /^(\w{3,4}\-\d+)/ ) { print “worm gene $1\n”; }}

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A parser for output from a gene prediction program

Putting it all together

GlimmerM (Version 3.0)Sequence name: BAC1Contig11Sequence length: 31797 bp

Predicted genes/exons

Gene Exon Strand Exon Exon Range Exon # # Type Length

1 1 + Initial 13907 13985 79 1 2 + Internal 14117 14594 478 1 3 + Internal 14635 14665 31 1 4 + Internal 14746 15463 718 1 5 + Terminal 15497 15606 110

2 1 + Initial 20662 21143 482 2 2 + Internal 21190 21618 429 2 3 + Terminal 21624 21990 367

3 1 - Single 25351 25485 135

4 1 + Initial 27744 27804 61 4 2 + Internal 27858 27952 95 4 3 + Internal 28091 28576 486 4 4 + Internal 28636 28647 12 4 5 + Internal 28746 28792 47 4 6 + Terminal 28852 28954 103

5 3 - Terminal 29953 30037 85 5 2 - Internal 30152 30235 84 5 1 - Initial 30302 30318 17

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while(<>) { if(/^(Glimmer\S*)\s+\((.+)\)/ { $method = $1; $version = $2; } elsif( /^(Predicted genes)|(Gene)|(\s+\#)/ || /^\s+$/ ) { next } elsif( # glimmer 3.0 output /^\s+(\d+)\s+ # gene num (\d+)\s+ # exon num ([\+\-])\s+ # strand (\S+)\s+ # exon type (\d+)\s+(\d+) # exon start, end \s+(\d+) # exon length /ox ) {my ($genenum,$exonnum,$strand,$type,$start,$end, $len) = ( $1,$2,$3,$4,$5,$6,$7); }}

Putting it together

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Same as m// but will allow you to substitute whatever is matched in first section with value in the second section

$sport =~ s/soccer/football/

$addto =~ s/(Gene)/$1-$genenum/;

s/// operator (substitute)

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Match and replace what is in the first section, in order, with what is in the second.

lowercase - tr/[A-Z]/[a-z]/

shift cipher - tr/[A-Z]/[B-ZA]/

revcom - $dna =~ tr/[ACGT]/[TGCA]/; $dna = reverse($dna);

The tr/// operator (translate)

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aMino - {A,C}, Keto - {G,T}

puRines - {A,G}, prYmidines - {C,T}

Strong - {G,C}, Weak - {A,T}

H (Not G)- {ACT}, B (Not A), V (Not T), D(Not C)

$str =~ tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/;

(aside) DNA ambiguity chars