GT_Xhyb_CTGSIN-SS-mira_assembly_rep_c3140|919|60    TACATCCTCCAAAGGACAAGATCTTGCCTTCCTTGTTGGTAGAAAAAATGCCGAGAGCAG
GT_Specific_CTGSIN-SS-EX055483|266|60    TTCTACCTATCGTTTCGGCTCAAGTTAGTGTCAGCAAATGATCCGAACGGTCTGGAAATG
GT_Specific_CTGSIN-SS-CL15294Contig1|1386|60_New    TTTTCTTTATAAAGAACAGTCTGTGTGTTAATAATTCTCATCTCCTGTCCGGACATAGAC
GT_Xhyb_SUPCTG-SS-SuperContig_CL53Contig7|737|60    CGTTTGAATGTATGACATATGAACATCGTTGCTCTCCTTCATCTTTTATGTGTTTTGGTT
GT_Specific_CTGSIN-SS-CL11320Contig1|392|60    TACTCTTGTAAAACCTTATACATACTTGCACATAAGAGAAAGATGGGATGTATTTCACAA
.......

mira_assembly_rep_c5    AT4G25140.1    OLEO1 (OLEOSIN 1) 
mira_assembly_rep_c8    AT4G27140.1    2S seed storage protein 1 / 2S albumin storage protein / NWMU1-2S albumin 1 
mira_assembly_rep_c24    AT5G38195.1    protease inhibitor/seed storage/lipid transfer protein (LTP) family protein 
mira_assembly_rep_c29    AT5G39850.1    40S ribosomal protein S9 (RPS9C) 
mira_assembly_rep_c36    AT4G32100.1    galactosyltransferase 
......

GT_Xhyb_CTGSIN-SS-mira_assembly_rep_c3140|919|60    TACATCCTCCAAAGGACAAGATCTTGCCTTCCTTGTTGGTAGAAAAAATGCCGAGAGCAG    mira_assembly_rep_c3140 AT4G25140.1    OLEO1 (OLEOSIN 1) 
GT_Specific_CTGSIN-SS-mira_assembly_rep_c5|266|60    TTCTACCTATCGTTTCGGCTCAAGTTAGTGTCAGCAAATGATCCGAACGGTCTGGAAATG   mira_assembly_rep_c5 AT4G10270.1    wound-responsive family protein 
GT_Specific_CTGSIN-SS-mira_assembly_rep_c8|1386|60_New    TTTTCTTTATAAAGAACAGTCTGTGTGTTAATAATTCTCATCTCCTGTCCGGACATAGAC   -mira_assembly_rep_c8 AT2G33830.2    dormancy/auxin associated family protein 
GT_Xhyb_SUPCTG-SS-SuperContig_mira_assembly_rep_c29|737|60    CGTTTGAATGTATGACATATGAACATCGTTGCTCTCCTTCATCTTTTATGTGTTTTGGTT mira_assembly_rep_c29   AT3G49910.1    60S ribosomal protein L26 (RPL26A)
......

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


my %line2;
my $merged;
my $count2;
my $col1=0;                 #The common column in file1
my $col2=0;                 #The common column in file2
my ($f1,$f2)=@ARGV;             #The two files to be merged
open(F2,$f2) or die $!; 
while (<F2>) { 
    s/\r?\n//;                 #remove return of carriage at the end of each line;
    my @F=split /\t/, $_;             #split the line by tab
    $line2{$F[$col2]} .= "$_\n"; }         #create a hash to store the line

$count2 = $.;                     #input line number
    
open(F1,$f1) or die $!; 
    while (<F1>) { 
        s/\r?\n//; 
        my @F=split /\t/, $_; 
        my $x = $line2{$F[$col1]}; 
            if ($x =~ m/$F[$col2]\|/) { 
            my $num_changes = ($x =~ s/^/$_\t/gm);     #substitute the beginning of the line with  
                                #the current line plus TAB
            print $x; 
             $merged += $num_changes;
            } 
    } 
    
warn "Joining $f1 column $col1 with $f2 column $col2\n$f1: $. lines\n$f2: $count2 lines\nMerged file: $merged lines\n";

# usage: match_script.pl file1 file2 > merged_file.tab