UNIX for Dummies Questions & Answers

#!/usr/bin/perl

use strict;
use warnings;

open (my $index_1 , '<', $ARGV[0]);
my %index_1;
while (<$index_1>){
        chomp;
        if (/^([CAGT]+)\s(\d+)$/){
                $index_1{$1}=$2;
        }
        else {
                print "Invalid input \"$_\" in $ARGV[0], line $.\n";
        }
}
close $index_1;

open (my $index_2 , '<', $ARGV[1]);
my %index_2;
while (<$index_2>){
        chomp;
        if (/^([CAGT]+)\s(\d+)$/){
                $index_2{$1}=$2;
        }
        else {
                print "Invalid input \"$_\" in $ARGV[1], line $.\n";

        }
}
close $index_2;
my %indices;
@indices{(keys %index_1),(keys %index_2)}++;
for my $index (sort (keys %indices)){
        print "$index\t ",$index_1{$index}||"0","\t", $index_2{$index}||"0","\n";
}

~/src/Perl/tmp$ perl test.pl file_1.dat file_2.dat
AAAA     5      0
AAAG     1      2
AATG     20     20
CATG     10     100
CCCC     0      1000
~/src/Perl/tmp$

@indices{(keys %index_1),(keys %index_2)}++;

#!/usr/bin/perl

use strict;
use warnings;

open (my $index_1 , '<', $ARGV[0]);
my %index_1;
while (<$index_1>){
        chomp;
        if (/^([CAGT]+)\s(\d+)$/){
                $index_1{$1}=$2;
        }
        else {
                print "Invalid input \"$_\" in $ARGV[0], line $.\n";
        }
}
close $index_1;

open (my $index_2 , '<', $ARGV[1]);
my %index_2;
while (<$index_2>){
        chomp;
        if (/^([CAGT]+)\s(\d+)$/){
                $index_2{$1}=$2;
        }
        else {
                print "Invalid input \"$_\" in $ARGV[1], line $.\n";

        }
}
close $index_2;

open (my $index_3 , '<', $ARGV[2]);
my %index_3;
while (<$index_3>){
        chomp;
        if (/^([CAGT]+)\s(\d+)$/){
                $index_3{$1}=$2;
        }
        else {
                print "Invalid input \"$_\" in $ARGV[2], line $.\n";

        }
}
close $index_3;



my %indices;
@indices{(keys %index_1),(keys %index_2),(keys %index_3)}++;
for my $index (sort (keys %indices)){
        print "$index\t ",$index_1{$index}||"0","\t", $index_2{$index}||"0","\n", $index_3{$index}||"0","\n";
}

AAAAAAACGTCAGGGAAGCTTGTCATG	 3	0
0
AAAAAACCGCCGATGCCTCCGGCCATG	 2	0
0
AAAAAAGTTTTAATCATTATCGACATG	 1	0
0
AAAAACTGTATTCAGTGACCAATCATG	 4	0
0
AAAAAGACAGCTGCTCCAGATAACATG	 1	0
0
AAAAATCTGTAAGGCTAATGGTGCATG	 1	0
0
...

#!/usr/bin/perl

use strict;
use warnings;
my @aoh; # array of hashes
for my $file (@ARGV){
        push (@aoh,include_data($file));
}
report(@aoh);
exit 1;

sub include_data{
        my $file=shift;
        open (my $index , '<', $file);
        my %index;
        while (<$index>){
                chomp;
                if (/^([CAGT]+)\s+(\d+)$/){
                        $index{$1}=$2;
                }
                else {
                        print "Invalid input \"$_\" in $ARGV[0], line $.\n";
                }
        }
        close($index);
        return \%index;
}
sub report{
        my @aoh=@_;
        my %indices;
        for my $index_ref (@aoh){
                @indices{keys %{$index_ref}}++;
        }
        for my $index (keys %indices){
                print "$index\t";
                for my $index_ref (@aoh){
                        print $index_ref->{$index}||0,"\t";
                }
                print "\n";
        }
}