Master perl io_2011

Read and Write Files
with Perl

Bioinformatics master course, „11/‟12 Paolo Marcatili

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


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


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


Conditions
if (condition){
Do something
}


Conditions
if ($time>5){
print “Time to go!n”;
}


Conditions
if ($day == 27){
print “Wage!n”;
}


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

print “snoozen”;

}


Perl IO

(IO means Input/Output)


Why IO?
Since now, Perl is

#! /usr/bin/perl -w
use strict; #<- ALWAYS!!!
my $string=”All work and no play makes Jack a
dull boyn";
for (my $i=1;$i<100;$i++){
print $string;
}


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


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

IO can do this!


IO types
Main Inputs
• Keyboard
• File
• Errors
Main outputs
• Display
• File


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;
}


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”


Handles
Handles are just streams “nicknames”
Some of them are fixed:
STDIN <-default is keyboard
STDOUT <-default is display
STDERR <-default is display
Some are user defined (files)


Open/Write a file


open
We have to create a handle for our file
open(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


close
When finished we have to close it:
close OUT;

If you dont, Santa will bring no gift.


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


Read from Files


Read
open(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;


Read with loops
Problems:
• It‟s long
• File size unknown

solution:
Use loops


While loop


While

while (condition){
do something…

}


While - for differences
While For

• Undetermined > Determined
• No counter > Counter


While example
Approx. 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 $solnError=$errn”;
}

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;


Redirect outputs


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

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

close(STDOUT);
close(STDERR);


@ARGV


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 !


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.


$_
• Perl default scalar value that is used when a
variable is not explicitly specified.
• Can be used in
– For Loops
– File Handling
– Regular Expressions


$_ and For Loops
• Example using $_ in a for loop

@array = ( “Perl”, “C”, “Java” );
for(@array) {
print $_ . “is a language I known”;
}

– Output :
Perl is a language I know.
C is a language I know.
Java is a language I know.


$_ 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 $_


Opendir, readdir


Opendir& readdir
• Just like open, but for dirs

# load all files of the "data/" folder into the @files array
opendir(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>";


Master perl io_2011

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