PerlScripting

Writing Perl Scripts

Boyce Thompson Institute for Plant
Research
Tower Road
Ithaca, New York 14853-1801
U.S.A.

by
Aureliano Bombarely Gomez

Writing Perl Scripts:
1. Four mandatory lines.

2. Useful modules I: Files.

3. Useful modules II: Options.

4. Documentation and being verbose.

5. Exercise: Assembly stats.


1.LINE: #!/usr/bin/perl
Where ? At the beginning of the script.
Why ? It says to the operating system what
program needs to use to executate the script .

2.LINE: use warnings;
Where ? Before declare the modules and variables.
(sooner is better).
Why ? It will print any compilation warnings.

3.LINE: use strict;
Where ? Before declare the modules and variables.
(sooner is better).
Why ? It will check any gramatical error and it will not
Let run scripts with errors.


4.LINE: 1;
Where ? At the end of the script.
Why ? It says to the operating system that the script
It is done.

#!/usr/bin/perl

use strict;
use warnings;

###########
## MY CODE
###########

1;

2. Useful modules I: Files

JUST A REMINDER: How open/Read/Write/Close files.

1. OPEN FUNCTION.

open (FILEHANDLE, MODE, REFERENCE);

FILEHANDLES: undefined scalar variable autovivified.

MODE: read, input only: <
write, output only: >
append to a file: >>
read/write update access: +<
write/read update access +>
read/append update access +>>

REFERENCE: Filename or reference to open



1. OPEN FUNCTION.

open (my $ifh, '<', $input_filename);
open (my $ofh, '>', $output_filename);

SUGGESTIONS: “use autodie” instead “OR die(“my error”)”;

open (my $ifh, '<', $input_filename)
OR die(“ERROR OPENING FILE: $!”);



2. READING OPENED FILES.
while(<FILEHANDLE>) {
## BLOCK USING $_ as LINE (don't forget chomp)
}

SUGGESTIONS: “Know the status of the file”

my @filelines = <FILEHANDLE>;
my $L = scalar(@filelines);
my $l = 0;

foreach my $line (@filelines) {
$l++;
print STDERR “Reading line $l of $L lines r”;
}



3. WRITE OVER OPENED FILES.

print $ofh “This to print over the file”;

4. CLOSE FILES.

close($ofh);


a) File::Basename;

Parse file paths into directory, filename and suffix.

use File::Basename;

my ($name, $path, $suffix) = fileparse($fullname,@suffixlist);

my $name = fileparse($fullname, @suffixlist);

my $basename = basename($fullname, @suffixlist);

my $dirname = dirname($fullname);


b) File::Spec;

Operations over filenames.

use File::Spec;

my $currdir = File::Spec->currdir();
my $tempdir = File::Spec->tempdir();

my $path = File::Spec->catfile($currdir, $filename);

3. Useful modules II: Options

Usual way to pass options: Using $ARGV

user@comp$ myscript.pl argument1 argument2

#!/usr/bin/perl

use strict;
use warnings;
use autodie;

my ($arg1, $arg2) = @ARGV;

1;


Usual way to pass options: Using $ARGV

PROBLEM:

When there are multiple arguments can be confusing.

Mandatory arguments are difficult to check !!!

SOLUTION:

Use modules GetOpt::Std or GetOpt::Long


GetOpt::Std;

Process single-character arguments from the command line

user@comp$ myscript.pl -i argument1 -o argument2 -V -H
use GetOpt::Std;

our( $opt_i, $opt_o, $opt_V, $opt_H);
getopts(i:o:VH);

## i: and o: expect something aftter the switch.
my $input = $opt_i || die(“ERROR: -i <input> was not supplied.”);
my $output = $opt_i || die(“ERROR: -o <output> was not supplied.”);

## V and H don't expect anything after the switch.
if ($opt_H) {
print $help;
}

4. Documentation and being verbose

Three types of documentation:

1) Document code with #.
GOOD: Useful for developers.
BAD: Inaccessible for users if they not open the script.

2) Document using perldoc.
GOOD: Clear and formated information.
BAD: perdoc is not always installed in the system.

3) Document using an inside print function.
GOOD: Frecuently easy to access. Intuitive.
BAD: ??? Well increase the size of your script.


Documenting through a function;
sub help {

print STDERR <<EOF;
$0:
Description:
My program description.

Synopsis:
myscript.pl [-H] [-V] -i <input>

Arguments:
-i <input> input file (mandatory)
-H <help> print Help.
-V <verbose> be verbose

EOF;
Exit(1);
}


Calling help;

use GetOpt::Std;

getopts(i:o:VH);


## V and H don't expect anything after the switch.
if ($opt_H) {
help();
}


Being verbose;

use GetOpt::Std;

getopts(i:o:VH);


if ($opt_V) {
my $date = `date`;
chomp($date);
print STDERR “Step 1 [$date]:ntParsing -i $input file.n”;
}


Being verbose;

my @filelines = <FILEHANDLE>;
my $L = scalar(@filelines);
my $l = 0;

foreach my $line (@filelines) {
$l++;
if ($opt_V) {
print STDERR “Reading line $l of $L lines r”;
}
}

5. Exercise: Assembly Stats

GOAL: Create a script to calculate:

1) Number of sequence in a file.

2) Total BP of a file.

3) Longest sequence

4) Shortest sequence.

5) Average and SD.

6) N25, N50, N75, N90, N95 (length and indexes)

5. Exercise: Assembly Stats

6) N25, N50, N75, N90, N95 (length and indexes)

Just a reminder:

N50 Length is the minimun length contained by the
50% of the size of the file (in bp) when it is ordered
by decreasing length.

N50 Index is the number os sequences contained by the
50% of the size of the file (in bp) when it is ordered
by decreasing length.

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