Perl snippets #perl

Arguments

#!/usr/bin/perl

use Getopt::Long;

my ($opt_help, $opt_version, $opt_input);
my $result = GetOptions(
    'i|input=s' => \$opt_input,
    'version'   => \$opt_version,
    'help'      => \$opt_help
);
 

avg.pl

sub stdev {
 
 	my $number_list_reference = shift @_;

	my $sum = 0; 
    my $delta = 0; 
    my $count = 0; 
    my $mean = 0; 
    my $stddev = 0;
 
	foreach $number (@{$number_list_reference}) {
		$count++;
		$delta = $number - $mean;
		$mean = $mean + ($delta / $count);
		$sum = $sum + $delta*($number - $mean);
	}
	return (0,0) if ($count == 1);
	$stddev = sqrt($sum/($count - 1));
 
    #return(sprintf("%.2f", $stddev), sprintf("%.2f",$mean));
	
	return($stddev , $mean);
 
 
}

Colors.pl

use Term::ANSIColor  qw(:constants);
print BOLD, BLUE, "This text is in bold blue.\n", RESET;
 
{
        local $Term::ANSIColor::AUTORESET = 1;
        print BOLD BLUE "This text is in bold blue.\n";
        print "This text is normal.\n";
}

file_basename.pl

use File::Basename;
 
# if $path = '/lustre/projects/myfolder/file.ext'...
 
my $base = basename($path);
my $dir  = dirname($path);
my ($base, $dir, $ext) = fileparse($path);

format_seconds.pl

sub formatsec { 
  my $time = shift; 
  my $days = int($time / 86400); 
  $time -= ($days * 86400); 
  
  my $hours = int($time / 3600); 
  $time -= ($hours * 3600); 
  
  my $minutes = int($time / 60); 
  
  my $seconds = $time % 60; 
 
  $days = $days < 1 ? '' : $days .'d '; 
  $hours = $hours < 1 ? '' : $hours .'h '; 
  $minutes = $minutes < 1 ? '' : $minutes . 'm '; 
  $time = $days . $hours . $minutes . $seconds . 's'; 
  return $time; 
}

Perl_POD.pl

#!/usr/bin/perl

use Pod::Usage;
my ($opt_help);

pod2usage({-exitval => 0, -verbose => 2}) if $opt_help;

__END__
 
=head1 NAME
 
B<Bold program name> - this program does this
 
=head1 AUTHOR
 
Andrea Telatin <andrea@telatin.com>
 
=head1 SYNOPSIS
 
this.pl --kmer=KMERLEN --peak=PEAK --fastq=FASTQ [--fastq=FASTQ]
 
=head1 DESCRIPTION
 
After running jellyfish with a particular KMERLEN and one or more FASTQ files,
determine the PEAK using jellyplot.pl and find_valleys.pl. Next, use this
PEAK as well as the KMERLEN and the FASTQ files used in the jellyfish run
as input. The script will determine the coverage and genome size.
 
=head1 TYPICAL SESSION
 
=over 2
 
# count k-mers (see jellyfish documentation for options)
gzip -dc reads1.fastq.gz reads2.fastq.gz | jellyfish count -m 31 -o fastq.counts -C -s 10000000000 -U 500 -t 30 /dev/fd/0
 
# generate a histogram
jellyfish histo fastq.counts_0 > fastq.counts_0.histo
 
# generate a pdf graph of the histogram
jellyplot.pl fastq.counts_0.histo
 
# look at fastq.counts_0.histo.pdf and identify the approximate peak
 
# use find_valleys.pl to help pinpoint the actual peak
find_valleys.pl fastq.counts_0.histo
 
# estimate the size and coverage
estimate_genome_size.pl --kmer=31 --peak=42 --fastq=reads1.fastq.gz reads2.fastq.gz
 
=back
 
=head1 BUGS
 
Please report them to <andrea@telatin.com>
 
=head1 COPYRIGHT
 
Copyright (C) 2013 Andrea Telatin 
 
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
 
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
 
You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
=cut