#!/usr/bin/perl -w use strict; use warnings; use Text::CSV_XS; open (my $FILE1, '<', "inputfile1.csv") or die "cannot open file1 $!\n"; open (my $FILE2, '<', "inputfile2.csv") or die "cannot open file2 $!\n"; open (my $FILE3, '<', "inputfile3.csv") or die "cannot open file3 $!\n"; open (my $FILE4, '>', "Outputfile.csv") or die "cannot open file4 $!\n"; my $csv = Text::CSV_XS->new ({ binary => 1, eol => $/ , sep_char => "\t", always_quote =>1}); my @columnheadings=split(/\t/,<$FILE1>); <$FILE2>; <$FILE3>; push (@columnheadings,('InFCDAC','InFCTriple')); my $headings=join("\t",@columnheadings); print $FILE4 "$headings\n"; my %file2; while (my $row = $csv->getline($FILE2)) { # chomp $row; my @fields = @$row; my $id = $fields[0]; $file2{$id}=["",@fields]; #print "$id\n"; } my %file3; while (my $row = $csv->getline($FILE3)) { # chomp $row; my @fields = @$row; my $id = $fields[0]; $file3{$id}=["",@fields]; #print "$id\n"; } while (my $row=$csv->getline($FILE1)) { my @fields=@$row; my $id=$fields[0]; if (exists $file2{$id}) { if(exists $file3{$id}) { my $fields_ref=\@fields; my @fields2=$file2{$id}[5]; my @fields3=$file3{$id}[5]; my @printline=$fields_ref."\t".\@fields2."\t".\@fields3; $csv->print ($FILE4,\@printline); } else { } } else { } }