Programming

ID File1
A 1
C 3
D 4
M 6

ID File2
A 5
B 10
C 15
Z 26

ID File3
A 2
B 6
O 20
X 9

ID  File File2 File3
A 1 5 2 
B 0 10 6
C 3 15 0
D 4 0 0
M 6 0 0 
O 0 0 20
X 0 0 9
Z 0 26 0

#!/usr/bin/perl -w

use strict;

my $Fname1="./path/file1.txt"; #tab delimited format 
my $Fname2="./path/file2.txt";
my $Fname3="./path/file3.txt";

my %combinedfile;
my key;

open(F1, "<$Fname1") or die "Cann't find the input file $Fname1 becuase of $!";
while (my line1 = <F1>) {
  chomp ($line1);
my ($ID1, $count)=split("\t", $line1);
$key=$ID1;
$combinedfile{$key}=$count;
}
close (F1);

open(F2, "<$Fname2") or die "Cann't find the input file $Fname1 becuase of $!";
while (my line2 = <F2>) {
  chomp ($line2);
my ($ID2, $count2)=split("\t", $line2);
$key=$ID2;
if (exists($combinedfile{$key}
 { $combinedfile{$key}.="\n$count2";}
else {
 $combinedfile{$key}="0\n$count2";
}
close (F2);

open(F3, "<$Fname3") or die "Cann't find the input file $Fname1 becuase of $!";
 while (my line3 = <F3>) {
   chomp ($line3);
 my ($ID3, $count3)=split("\t", $line3);
 $key=$ID3;
if (exists($combinedfile{$key}
 { $combinedfile{$key}.="\n$count3";}
else {
 $combinedfile{$key}="0\n0\n$count3";
}
close (F3);

foreach (my $member (keys %combinedfile)){
 split ("/n", $combinedfile{$member));
print $member, "\t", (join("\t", split ("/n", $combinedfile{$member)), "\n";
}

 ID File File2 File3
A 1 5 2 
B 0 10 6
C 3 15 
D 4
M 6
O 0 0 20
X 0 0 9
Z 0 26

D 4\n0

D 4\n0\n0

join -a 1 -a 2 -e 0 -o0,1.2,2.2 f1 f2 |join -a 1 -a 2 -e 0 -o0,1.2,1.3,2.2 - f3

./yourscript.pl file1.txt file2.txt file3.txt

#!/usr/bin/perl -w

use strict;

my %combinedfile = ();
my @file_list = ();

foreach my $file (@ARGV)
{
    my $basename = substr($file, rindex($file, '/') + 1);
    my $name = uc(substr($basename, 0, rindex($basename, '.')));
    push(@file_list, $name);

    if (open(F, $file))
    {
        while (my $line = <F>)
        {
            chomp($line);

            my @item = split("\t", $line);
            my $id = defined($item[0]) ? $item[0] : '';
            my $count = defined($item[1]) ? $item[1] : 0;
            next if ($id eq '');

            $combinedfile{$id} = () if (!defined($combinedfile{$id}));
            $combinedfile{$id}->{$name} = 0 if (!defined($combinedfile{$id}->{$name}));
            $combinedfile{$id}->{$name} = $count;
        }

        close(F);
    }
}

print "ID";

foreach my $name (@file_list)
{
    print "\t$name";
}

print "\n";

foreach my $id (sort keys %combinedfile)
{
    print "$id";

    foreach my $name (@file_list)
    {
        my $count = defined($combinedfile{$id}->{$name}) ? $combinedfile{$id}->{$name} : 0;
        print "\t$count";
    }

    print "\n";
}

exit(0);

 while (my $line = <F>){            
chomp($line);              
my @item = split("\t", $line);                                # Understand
my $id = defined($item[0]) ? $item[0] : '';             #Start to get lost, the purpose of the empty string
my $count = defined($item[1]) ? $item[1] : 0;           #??? if there is no count there, how can I assign $item[1] with 0. Biggest trick
next if ($id eq '');             
$combinedfile{$id} = () if (!defined($combinedfile{$id}));
$combinedfile{$id}->{$name} = 0 if (!defined($combinedfile{$id}->{$name}));
$combinedfile{$id}->{$name} = $count;      
}

Use of uninitialized value in string eq at ...

my ($id, $count) = split("\t", $line);

 $combinedfile{$id} = () if (!defined($combinedfile{$id}));
 $combinedfile{$id}->{$name} = 0 if (!defined($combinedfile{$id}->{$name}));
 $combinedfile{$id}->{$name} = $count;

 

# Add "id" to "$combinedfile" and initialize the element as a hash
$combinedfile{$id} = () if (!defined($combinedfile{$id}));

# Add "name" to "$combinedfile{$id}" and initialize the element as an integer zero
 $combinedfile{$id}->{$name} = 0 if (!defined($combinedfile{$id}->{$name}));

# Assign the value to the element
 $combinedfile{$id}->{$name} = $count;