#!/usr/bin/perl

use strict;
use warnings;


my $usage = "perl mgf_rt.pl [input mgf file] [mascot csv output] [output file]\n";
my $mgfin = shift or die $usage;
my $csvin = shift or die $usage;
my $output = shift or die $usage;
my @IDS;

open (CSV, '<', $csvin);

while (my $line = <CSV>){
    chomp $line;
    my $id = 'initial';
    if($line =~ /([^,]*,){30}"([^"]*)/){$id = $2;
    push (@IDS, $id);
    }
}

close CSV;

print "Finished collecting spectra names from CSV file\n";

open (MGF, '<', $mgfin);

my $A = '0';
my $B = '0';
my $TI = 'initial';
my $RT = 'initial';
my %IDrtPairs;

while (my $line = <MGF>){
    if ($line =~ /TITLE=(.*)/){$TI="$1"; 
			       $A = '1';
    }
    if ($line =~ /RTINSECONDS=(.*)/){$RT="$1";
				     $B = '1';
    }
    if ($A+$B == 2 && grep {$_ eq $TI} @IDS){
	$IDrtPairs{"$TI"}="$RT";
	$A = '0';
	$B = '0';
    }
}

close MGF;

print "Finished getting RT information from MGF file\n";

open (CSV, '<', $csvin);

open (OUT, '>>', $output);

while (my $line = <CSV>){
    chomp $line;
    my $id = 'initial';
    if($line =~ /([^,]*,){30}"([^"]*)/){$id = $2;
					my $reten = "$IDrtPairs{$id}";
					print OUT  "$line,$reten\n";
    }else{
	print OUT "$line\n";
    }
}   

close CSV;
close OUT;

##</code><code>##

SEARCH=MIS
MASS=Monoisotopic
BEGIN IONS
TITLE=AE.36154.36154.2 (intensity=3533482168.8807)
PEPMASS=358.209301553256
CHARGE=2+
SCANS=36154
RTINSECONDS=1697.984
55.05507 86438.71
56.05026 89053.36
60.0452 843930.94
60.05638 100834.36
69.07059 82593.55
70.02967 63427.3
70.0659 1222576