master perl io_2011

Bioinformatics master course, ‘11/’12

Paolo Marcatili

Read and Write Fileswith Perl


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Resume

• Scalars $• Arrays @• Hashes %• Foreach |-@ $ • Length …• Split $ @


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Agenda

• For• Conditions• Perl IO• Open a File• Write on Files• Read from Files• While loop


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New cycle!

for (my $i=0;$i<100;$i++){print “$i \n”;

}

Can we rewrite foreach using for?

Hint: scalar @array is the array size


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Conditions

if (condition){Do something}


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Conditions

if ($time>5){print “Time to go!\n”;}


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Conditions

if ($day == 27){print “Wage!\n”;}


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Conditions

if ($day eq “Sunday”){print “Alarm off!\n”;}else{

print “snooze\n”;

}


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Perl IO

(IO means Input/Output)


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Why IO?

Since now, Perl is

#! /usr/bin/perl -w

use strict; #<- ALWAYS!!!my $string=”All work and no play makes Jack

a dull boy\n";for (my $i=1;$i<100;$i++){ print $string;}


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Why IO?

But if we want to do the same with a user-submitted string?


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Why IO?

But if we want to do the same with a user-submitted string?

IO can do this!


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IO types

Main Inputs• Keyboard• File• ErrorsMain outputs• Display• File


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More than tomatoes

Let’s try it:

#! /usr/bin/perl -w use strict; my $string=<STDIN>;

for (my $i=1;$i<100;$i++){print $string;

}


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Rationale

Read from and write to different media

STDIN means standard input (keyboard)

^ this is a handle

<SMTH> means “read from the source corresponding to handle

SMTH”


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Handles

Handles are just streams “nicknames”Some of them are fixed:STDIN <-default is keyboardSTDOUT <-default is displaySTDERR <-default is displaySome are user defined (files)


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Open/Write a file


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open

We have to create a handle for our fileopen(OUT, “>”,”out.txt”) or die(“Error opening

out.txt: $!”);

^N.B. : it’s user defined, you decide it

Tip“<“,”out.txt” <- read from out.txt “>”,”out.txt” <- write into out.txt “>>”,”out.txt” <- append to out.txt


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close

When finished we have to close it: close OUT;

If you dont, Santa will bring no gift.


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Print OUT

#! /usr/bin/perl -w

use strict;open(OUT, ">”,”out.txt") || die("Error opening

out.txt: $!");print "type your claim:\n";my $string=<STDIN>;for (my $i=1;$i<100;$i++){ print OUT $string;}close OUT;

Now let’s play with <,>,>> and file permissions


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Read from Files


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Readopen(IN, “<song.txt”) or die(“Error opening song.txt: $!”);print <IN>;print <IN>;print <IN>;print <IN>;print <IN>;print <IN>;print <IN>; print <IN>;print <IN>; print <IN>;print <IN>; print <IN>;print <IN>; print <IN>;

close IN;


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Read with loops

Problems:• It’s long• File size unknown

solution:Use loops


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While loop


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While

while (condition){ do something…

}


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While - for differences

While

• Undetermined

• No counter

For

> Determined> Counter


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While exampleApprox. solution of x^2-2=0(Newton’s method)

my $sol=0.5;my $err=$sol**2-2;while ($err**2>.001){$sol-=($sol**2-2)/(2*$sol);$err=$sol**2-2;print “X is $sol\nError=$err\n”;}


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Read with while

#! /usr/bin/perl -w

use strict;open(MOD, "<IG.pdb") || die("Error

opening IG.pdb: $!");

while (my $line=<MOD>){ print substr($line,0,6)."\n";}close MOD;


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Redirect outputs


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Redirections

#!/usr/bin/perlopen(STDOUT, ">foo.out") || die "Can't redirect stdout";open(STDERR, ">&STDOUT") || die "Can't dup stdout";

select(STDERR); $| = 1; # make unbufferedselect(STDOUT); $| = 1; # make unbuffered

close(STDOUT);close(STDERR);


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@ARGV


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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 -1 !


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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.


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$_

• Perl default scalar value that is used when a variable is not explicitly specified.

• Can be used in– For Loops– File Handling– Regular Expressions


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$_ 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.


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$_ 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 $_


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Opendir, readdir


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Opendir & readdir• Just like open, but for dirs

# load all files of the "data/" folder into the @files arrayopendir(DIR, ”$ARGV[0]");@files = readdir(DIR);closedir(DIR); # build a unsorted list from the @files array:print "<ul>"; foreach $file (@files) { next if ($file eq "." or $file eq ".."); print "<li><a href=\"$file\">$file</a></li>";} print "</ul>";

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