Athanasius, this was a great help! Thank you. In fact, I expect that file 2 will be quite large so this method should work better.

I have an additional question related to this code but I don't know whether it should be posted here or as a new post. I will chance asking here and remove it if there is a problem. I want to ensure that for Sample_2A, Sample_2B, Sample_2C in file_1 each of these columns will be compared to Sample_2 in file 2 i.e. that columns with matching numbers are compared but I am not sure of the best way to do this but in the code you suggested it might be difficult to do this since the fields are broken up line-by-line

Hello again, corcra,

I’m glad to have been of help.

If I understand you correctly, you now want read the data headings, say:

Field:    0            5            6            7            8
File 1: ['CHROM', ... 'SAMPLE_1A', 'SAMPLE_1B', 'SAMPLE_2A', 'SAMPLE_2
+B']
File 2: ['CHROM', ... 'SAMPLE_1',  'SAMPLE_2',  'SAMPLE_3']
[download]

and have the script deduce that File 1 data in fields 5 and 6 should each be compared to File 2 field 5, File 1 data in fields 7 and 8 should each be compared to File 2 field 6, and so on.

That makes the logic more complex, but I don’t know why you think this will be difficult to do line-by-line? Most of the added logic comes before the big while loop:

Read more... (1133 Bytes)

The main addition is a hash (%index_map) to keep track of the correspondences between the fields in File 1 and the matching fields in File 2.

Hope that helps,

Athanasius <°(((>< contra mundum

Iustus alius egestas vitae, eros Piratica,

Hi Athanasius, Hope you are well and thank you for all of your help so far. Unfortunately I still have not been able to get the code working as I want it to and I was hoping you could have one further look at the code I am running. The format of my input files has changed slightly but I don't think this will affect the code too much.

File 1
CHROM    POS    REF    ALT    VARIANT_LIST    209T-D  459T-D    644T-D
+    94T-D    99T1-D    99T2-D    99T3-D    99T4-D    99T5-D    
['MT', '1010', 'G', 'A', 'A', 'REF', 'A', 'A', 'REF', 'A', 'A', 'A', '
+A', 'A']
['MT', '2962', 'C', 'T', 'T', 'REF', 'T', 'T', 'T', 'T', 'T', 'T', 'T'
+, 'T']
...
[download]

File 2 
CHROM     POS     REF     ALT     VARIANT_LIST    209H-D    459H-D    
+644H-D    94H-D    99H-D    
['MT', '1010', 'G', 'A', 'A', 'REF', 'REF', 'REF', 'REF', 'REF']
['MT', '2962', 'C', 'T', 'T', 'REF', 'REF', 'T', 'REF', 'T']
....
[download]

Again I want to compare 99T1, 99T2, 99T3, 99T4 and 99T5 of File1 with 99H of file 2. The output I want looks like

 
CHROM    POS    REF    ALT    VARIANT_LIST    209T-D  459T-D    644T-D
+    94T-D    99T1-D    99T2-D    99T3-D    99T4-D    99T5-D    
['MT', '1010', 'G', 'A', 'A', 'REF', 'A', 'A', 'REF', 'A', 'A', 'A', '
+A', 'A']
['MT', '2962', 'C', 'T', 'T', 'REF', 'T', 'REF, 'T', 'REF', 'REF', 'RE
+F', 'REF', 'REF']
[download]

(because the same letter at the same position in File 1 and File 2 should output REF, and if REF is found at that position in file 2, just output letter from File 1) The code I am currently running is:

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

my $file1 = shift;
my $file2 = shift;

open(my $in1, '<', $file1)
    or die "Cannot open file '$file1' for reading: $!";

open(my $in2, '<', $file2)
    or die "Cannot open file '$file2' for reading: $!";

my $header1 = <$in1>;
<$in2>;
my @heads1  = split "\t", $header1;
my $index = 5;
my %index_map;

for (@heads1)
{
    $index_map{$index++} = $1 + 4 if m/^(\d+)/;
}

print $header1;
while (my $line1 = <$in1>)
{
    my @fields1 = get_fields($line1);

    defined(my $line2 = <$in2>)
        or die "Data missing in file '$file2': $!";

    my @fields2 = get_fields($line2);
    my @out     = @fields1;

 for my $i (5 .. $#fields1)
    {
    my $j = $index_map{$i};
        
    if ($fields1[$i] ne 'REF')
            {
        
            $out[$i] = $fields2[$j] if exists $fields2[$j] &&
                        $fields2[$j] ne 'REF';

        }

}
    @out = map { "'$_'" } @out;
    print '[', join(', ', @out), "]\n";
}

close $in2
    or die "Cannot close file '$file2': $!";

close $in1
    or die "Cannot close file '$file1': $!";

sub get_fields
{
    my ($line) = @_;

    chomp $line;
    my @fields = split "\t", $line;
    s{ ^ \[? ' }{}x for @fields;
    s{ ' \]? $ }{}x for @fields;

    return @fields;
}
[download]

which should work but the output is

CHROM    POS    REF    ALT    VARIANT_LIST    209T-D  459T-D    644T-D
+    94T-D    99T1-D    99T2-D    99T3-D    99T4-D    99T5-D    
['MT', '1010', 'G', 'A', 'A', 'REF', 'A', 'A', 'REF', 'A', 'A', 'A', '
+A', 'A']
['MT', '2962', 'C', 'T', 'T', 'REF', 'T', 'T', 'T', 'T', 'T', 'T', 'T'
+, 'T']
...
[download]

I really do not know what is going wrong? If you have any suggestions please let me know. Thanks!