I found the code a bit confusing and this tab delimited format is a bummer to work with. One of the problems will be that when you add "null" fields, if you don't quote these things, then it is really hard to see these fields in file3.

Anyway I would suggest using some version of Text::CSV to parse the data and you can adjust the quoting characters to your liking (this module helps on both input and output). Tabs will probably get mangled in example data below, but I think you'll get the idea. 

#!/usr/bin/perl -w
use strict;

use Text::CSV_XS;

open (my $FILE1, '<', "file1.csv") or die "cannot open file1 $!\n";
open (my $FILE2, '<', "file2.csv") or die "cannot open file3 $!\n";
open (my $FILE3, '>', "file3.csv") or die "cannot open file3 $!\n";

my $csv = Text::CSV_XS->new ({ binary => 1, eol => $/ , 
                               sep_char => "\t", always_quote =>1});

print $FILE3 "Match\t".<$FILE1>; # header for file3
<$FILE2>;                        # skip header line of file2

my %file1; 
my %file2;

while (my $row = $csv->getline($FILE1)) 
{
    my @fields = @$row;
    my $id = $fields[4];
    $file1{$id}=["",@fields];
}

while (my $row = $csv->getline($FILE2)) 
{
    my @fields = @$row;
    my $id = $fields[0];
    $file2{$id}=["","","","","",@fields,"","","","",""];
}

foreach my $id1 (keys %file1)
{
    if (exists $file2{$id1})
    {
        $file1{$id1}[0] ="both";             #both files
        $csv->print ($FILE3, $file1{$id1});
    }
    else
    {
        $file1{$id1}[0] ="1";                #file1 only
        $csv->print ($FILE3, $file1{$id1});
    }
}

foreach my $id2 (keys %file2)
{
    if (!exists $file1{$id2})
    {
        $file2{$id2}[0] ="2";               #file2 only
        $csv->print ($FILE3, $file2{$id2});
    }
}

[download]
file1: 
Group    Functional_Category    LT    IA    ID    Symbol    Descriptio
+n    TID    GID    LO    S1    S2    HL    Status    V1    V2    IN 
q    w    a    a    1    AA    some description    10    11    1    s1
+a    s2a    1    1    1    1    1
q    w    b    b    2    BB    another descrp    11    12    1    s1b 
+   s2b    1    1    1    1    1
q    w    c    c    5    CC    despript A    12    13    1    s1c    s
+2c    1    1    1    1    1

[download]
file2 
ID    Symbol    Description    TID    GID    LO    S1    S2 
2    BB    another descrp    11    12    1    s1b    s2b
4    DD    some more stuff    14    14    4    s1d    s2d

[download]
file3 
Match    Group    Functional_Category    LT    IA    ID    Symbol    D
+escription    TID    GID    LO    S1    S2    HL    Status    V1    V
+2    IN 
"1"    "q"    "w"    "a"    "a"    "1"    "AA"    "some description"  
+  "10"    "11"    "1"    "s1a"    "s2a"    "1"    "1"    "1"    "1"  
+  "1"
"both"    "q"    "w"    "b"    "b"    "2"    "BB"    "another descrp" 
+   "11"    "12"    "1"    "s1b"    "s2b"    "1"    "1"    "1"    "1" 
+   "1"
"1"    "q"    "w"    "c"    "c"    "5"    "CC"    "despript A"    "12"
+    "13"    "1"    "s1c"    "s2c"    "1"    "1"    "1"    "1"    "1"
"2"    ""    ""    ""    ""    "4"    "DD"    "some more stuff"    "14
+"    "14"    "4"    "s1d"    "s2d"    ""    ""    ""    ""    ""

[download]

In reply to Re: Issues with Column headings by Marshall
in thread Issues with Column headings by bluray

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