Hi, I have in this example 2 files, each of which is a 9 column file. Format of both the files are same. This is how my input dummy files look like: file1.tab

chr10    94055    94554    2    2    1    1    0    23
chr10    95850    122380    2    2    1    1    0    15
chr10    181243    196457    1    1    1    1    0    21
chr10    181243    225933    1    1    1    4    0    21
chr10    181500    225933    1    1    1    15    0    25
chr10    226069    255828    1    1    1    53    0    22
chr10    255948    267233    1    1    1    2    0    12
chr10    255989    267134    1    1    1    65    0    25
chr10    255989    282777    1    1    1    14    0    23
chr10    264440    267134    1    1    1    1    0    25
[download]

file2.tab

chr10    94055    94554    2    2    1    1    0    21
chr10    94055    94743    2    2    1    1    0    20
chr10    94666    94743    2    2    1    3    0    20
chr10    94853    95347    2    2    1    2    0    25
chr10    181243    225933    1    1    1    3    0    21
chr10    181500    225933    1    1    1    7    0    10
chr10    226069    255828    1    1    1    38    0    22
chr10    255989    267134    1    1    1    29    0    24
chr10    255989    282777    1    1    1    15    0    23
chr10    267297    282777    1    1    1    44    0    24
[download]

The columns in the files are tab separated. I want to combine the 2 files in a way that first 4 columns is used as a key and the value is the 7th column. If the key is missing in either file, the value for that key for that file should be 0. This is the output I would like:

chr    fivep    threep    strand    file1.tab    file2.tab
chr10    181500    225933    -    15    7
chr10    264440    267134    -    1    0
chr10    94055    94554    -    1    1
chr10    181243    225933    -    4    3
chr10    94666    94743    -    0    3
chr10    255989    282777    -    14    15
chr10    94853    95347    -    0    2
chr10    255948    267233    -    2    0
chr10    95850    122380    -    1    0
chr10    267297    282777    -    0    44
chr10    226069    255828    -    53    38
chr10    94055    94743    -    0    1
chr10    255989    267134    -    65    29
chr10    181243    196457    -    1    0
[download]

My code which is below, works perfectly fine, but I open my input files twice. Is there a way where I just have to open up the input files once? Code:

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

my @files = glob("file*.tab");
my %output = ();

foreach my $file ( @files ){
    open(my $fh,'<',$file) or die $!; 
    while(<$fh>){
        chomp;
        my @s = split /\t/;
        die("_ERROR_ not 9 columns [ $_ ]\n") if (@s != 9);
        $output{$s[0]."\t".$s[1]."\t".$s[2]."\t".$s[3]} = [];
    }
    close $fh;
}

foreach my $file ( @files ){
    
    foreach my $k(keys %output){
        push @{$output{$k}},0;
    }

        open(my $fh,'<',$file) or die $!;
        while(<$fh>){
        chomp;
                my @s = split /\t/;
                die("_ERROR_ not 9 columns [ $_ ]\n") if (@s != 9);

        my @array = @{$output{$s[0]."\t".$s[1]."\t".$s[2]."\t".$s[3]}}
+;

        $array[-1] = $s[6]; 

        $output{$s[0]."\t".$s[1]."\t".$s[2]."\t".$s[3]} = \@array;
    }
    close $fh;
}

print join("\t",'chr','fivep','threep','strand',@files),"\n";

foreach my $k(keys %output){
    my @s = split /\t/,$k;
    my $chr = $s[0];
    my $fivep = $s[1];
    my $threep = $s[2];
    my $strand = $s[3];
    next if($strand =~ /^0$/);
    if($strand =~ /^0$/){
        print join("\t",$chr,$fivep,$threep,"+",@{$output{$chr."\t".$f
+ivep."\t".$threep."\t".$strand}} ),"\n";
    }else{
        print join("\t",$chr,$fivep,$threep,"-",@{$output{$chr."\t".$f
+ivep."\t".$threep."\t".$strand}} ),"\n";
    }
}
[download]

I have several input files and many more lines than the current dummy files I have shown here.

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