BOL: Owner

Perl script to find missing and move to desire folder

Neel — Mon, 19 Mar 2018 12:35:54 -0500

#!/usr/bin/perl -w
use strict;
use warnings;
open(my $ids,  "<",  "$ARGV[0]")  or die "Can't open input.txt: $!";
while (<$ids>) {
chomp;
next if $_ =~ /^\s*$/;
my $id = $_;
	open(my $val,  "<",  "$ARGV[1]")  or die "Can't open input.txt: $!";

	while (<$val>)  {
	chomp;
	if (/$id/) {
	  print "found string $id\n";
	system ("cp $_ 2move"); 
	}

}


}

Perl script to extract the uniq Ids

Neel — Mon, 19 Mar 2018 12:34:19 -0500

#!/usr/bin/perl -w
use strict;
use warnings;
use List::Uniq ':all';

open(my $val,  "<",  "$ARGV[0]")  or die "Can't open input.txt: $!";
my @allMissed;
while (<$val>)  {
chomp;
my $flag=0;
next if $_ =~ /^\s*$/;
my $string = "$_";

open(my $file,  "<",  "$ARGV[1]")  or die "Can't open input.txt: $!";
while (<$file>)  {
	chomp;
	if (/$string/) {
	  #print "$string\n"; 
	$flag=1;
	}
}
close $file;
	if ($flag == 0) {
	push @allMissed, $string;
	}
}

close $val;

my @allRemaining = uniq (@allMissed);
foreach (@allRemaining) { print "$_\n";}

__END__

Extract the fastq sequence with range in Perl

Neel — Wed, 02 Aug 2017 04:29:06 -0500

use Bio::DB::Fasta;
open(POSITIONS,"positions.txt");
while(){
    chomp;
    my ($seqName,$begin,$end) = split(/\s/);
    my $db = Bio::DB::Fasta->new('allGenomeContacted.fa');
	my $seq = $db->seq("$seqName", $begin => $end);
	print "$seq\n";
}
close(POSITIONS);

Construct a heatmap with perl

Neel — Fri, 07 Jul 2017 04:35:13 -0500

#!/bin/env perl
use strict;
use warnings;

use Imager::Heatmap;

my $hmap = Imager::Heatmap->new(
    xsize  => 640,        # Image width
    ysize  => 480,        # Image height
    xsigma => 10,         # Sigma value of X-direction
    ysigma => 10,         # Sigma value of Y-direction
);

# @point_datas should be: ( [ x1, y1, weight1 ], [ x2, y2, weight2 ] ... )
my @point_datas = ( [ 10, 20, 50 ], [ 20, 40, 70 ] );

# Add point datas to construct density matrix
$hmap->insert_datas(@point_datas); 

# After adding datas, get heatmap as Imager instance.
my $img = $hmap->draw;

# create png file in current directory
$img->write( file => './hm.png' );

Perl script introduces control structures, arrays and hashes.

Neel — Mon, 04 Jul 2016 08:42:47 -0500

#!/usr/bin/env perl

use strict;
use warnings;

my @first_array = ('DNA', 'ATGCGTGC', 5, 'RNA', 'AUGC');
print $first_array[0], "\n\n";

# Scalar gives actual size of an array

my $size_of_array = scalar(@first_array);
my $another_way_of_getting_size_of_array = @first_array; # implicit way
print "Scalar of array: $size_of_array\n\n";
print "Perl's index size of array: $#first_array\n\n";
print "Another way of getting size: $another_way_of_getting_size_of_array\n\n";

# Control Loop: for

for (my $i=0; $i<=$#first_array; $i++) {
    print "Perl's array index: $i\n\n";
    print "$first_array[$i] \n\n"; 
}

my %sequence = ('DNA' => 'ATCGATGCT',
                'RNA' => 'AUGC',
                'Number of seqs' => 2
                );

print $sequence{'DNA'}, "\n";
# Control Loop: foreach

foreach my $key (sort (keys %sequence)) {
    print "Key of hash is $key\tValue of hash is $sequence{$key}\n\n";
}

Perl subroutine to read and write files

Neel — Thu, 30 Jun 2016 16:48:55 -0500

# Input output (InOut) the file
# usage:
# @array  = InOut('read',$file)
# $string = InOut('read',$file)
# InOut('write',$file,\$string)
# InOut('write',$file,\@array)
#$string = "YO!";
#InOut('write','file.txt',\$string);

sub InOut {
my($bit,$file,$data) = @_;

if($bit eq 'read'){
    open InOut,"< $file" or die "Cannot open $file for input: $!\n";
    my @file = ;
    close InOut;
    return wantarray ? @file :  join '', @file;
    }
if($bit eq 'write'){
    open  InOut,"> $file" or die "Cannot open $file for output: $!\n";
    print InOut  ref $data eq 'ARRAY' ? @$data : ref $data eq "SCALAR"? $$data : '';
    close InOut;
    }
}