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

#----PARAMETERS:

# histogram 
#
my @unsortedRepIons = 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# GlycoDB as released and reduced glycan masses: my @unsortedRepIons = (735.302968,751.297882,897.355791,913.350705,954.377255,993.317036,1059.408614,1075.403528,1100.435164,1116.430078,1155.369859,1157.456628,1196.396409,1221.461437,1237.456351,1246.493073,1262.487987,1278.482901,1303.514537,1317.422682,1319.509451,1358.449232,1383.51426,1397.389013,1399.509174,1407.525495,1408.545896,1423.520409,1424.54081,1440.535724,1449.572446,1465.56736,1479.475505,1481.562274,1520.502055,1522.588824,1553.583404,1559.441836,1561.561997,1569.578318,1570.598719,1585.573232,1586.593633,1595.630355,1600.468386,1602.588547,1610.604868,1611.625269,1626.599782,1627.620183,1641.528328,1643.615097,1668.646733,1682.554878,1684.641647,1699.641313,1715.636227,1721.494659,1723.61482,1725.668197,1731.631141,1732.651542,1747.626055,1748.646456,1756.662777,1757.683178,1762.521209,1764.64137,1772.657691,1773.678092,1788.652605,1789.673006,1803.547759,1803.581151,1805.66792,1814.704642,1830.699556,1844.607701,1846.69447,1861.694136,1871.726106,1877.68905,1885.667643,1887.72102,1893.683964,1894.704365,1902.720686,1909.678878,1910.699279,1918.7156,1919.736001,1924.574032,1928.74757,1934.710514,1935.730915,1950.705428,1951.725829,1960.762551,1965.600582,1967.720743,1975.737064,1976.757465,1991.731978,1992.752379,2006.660524,2008.747293,2017.784015,2023.746959,2033.778929,2039.741873,2047.720466,2048.778595,2049.773843,2055.736787,2063.753108,2064.773509,2071.731701,2074.805479,2079.748022,2080.768423,2081.788824,2090.800393,2095.742936,2096.763337,2097.783738,2106.82046,2112.758251,2113.778652,2121.794973,2122.815374,2127.653405,2129.773566,2137.789887,2138.810288,2153.784801,2154.805202,2163.841924,2170.800116,2178.816437,2179.836838,2185.799782,2194.811351,2195.831752,2201.794696,2209.773289,2209.811017,2210.831418,2211.826666,2217.78961,2220.863388,2225.805931,2226.826332,2236.858302,2241.800845,2242.821246,2252.853216,2257.795759,2258.81616,2259.836561,2267.852882,2268.873283,2274.811074,2275.831475,2283.847796,2284.868197,2293.879766,2299.84271,2300.863111,2309.899833,2315.837624,2316.858025,2324.874346,2325.894747,2332.852939,2340.86926,2341.889661,2355.868926,2356.864174,2357.884575,2366.921297,2371.826112,2371.86384,2372.884241,2373.879489,2381.89581,2382.916211,2387.858754,2388.879155,2397.890724,2398.911125,2403.853668,2404.874069,2413.910791,2414.906039,2419.848582,2420.868983,2428.885304,2429.905705,2430.926106,2436.863897,2439.937675,2444.880218,2445.900619,2446.92102,2455.932589,2455.957742,2460.875132,2461.895533,2462.915934,2470.932255,2471.952656,2477.890447,2478.910848,2486.927169,2487.94757,2494.905762,2501.926835,2502.922083,2503.942484,2512.979206,2517.921749,2518.916997,2519.937398,2527.953719,2528.97412,2533.916663,2535.932312,2543.948633,2544.969034,2549.911577,2550.931978,2559.943547,2559.9687,2560.963948,2565.906491,2566.926892,2574.943213,2575.963614,2576.958862,2581.901405,2582.921806,2585.995584,2590.938127,2591.958528,2592.978929,2601.990498,2606.933041,2607.953442,2608.973843,2616.990164,2617.985412,2618.010565,2622.927955,2623.948356,2624.968757,2631.964677,2632.985078,2634.005479,2639.94327,2640.963671,2647.959591,2648.979992,2650.000393,2659.011962,2659.037115,2663.954505,2663.979658,2664.974906,2665.995307,2674.011628,2675.032029,2679.974572,2680.96982,2681.990221,2690.006542,2691.026943,2695.969486,2697.985135,2706.001456,2707.021857,2711.9644,2721.001122,2721.99637,2722.021523,2723.016771,2727.959314,2732.053493,2736.996036,2738.016437,2739.011685,2747.028006,2748.048407,2752.99095,2754.011351,2763.02292,2763.048073,2764.043321,2768.985864,2770.006265,2778.022586,2779.042987,2780.038235,2780.063388,2784.980778,2786.001179,2794.0175,2795.037901,2796.058302,2801.996093,2805.069871,2810.012414,2811.032815,2812.053216,2820.069537,2821.064785,2821.089938,2826.007328,2827.027729,2828.04813,2835.04405,2836.064451,2837.084852,2843.022643,2844.043044,2851.038964,2852.059365,2853.079766,2860.037958,2867.033878,2867.059031,2868.054279,2869.07468,2878.111402,2882.033544,2883.053945,2884.049193,2884.074346,2885.069594,2893.085915,2894.106316,2898.028458,2899.048859,2900.06926,2901.064508,2909.080829,2909.105982,2910.10123,2914.023372,2915.043773,2916.064174,2924.080495,2925.075743,2925.100896,2926.096144,2930.018286,2931.038687,2932.059088,2940.075409,2941.09581,2942.091058,2942.116211,2947.033601,2948.054002,2951.12778,2956.070323,2957.090724,2958.111125,2966.127446,2967.122694,2972.065237,2973.085638,2974.106039,2981.101959,2982.12236,2983.117608,2983.142761,2988.060151,2989.080552,2990.100953,2997.096873,2998.117274,2999.137675,3005.075466,3006.095867,3013.091787,3013.11694,3014.112188,3015.132589,3022.090781,3024.144158,3024.169311,3028.091453,3029.086701,3029.111854,3030.107102,3031.127503,3039.143824,3040.164225,3044.086367,3045.106768,3046.102016,3047.122417,3055.138738,3056.159139,3060.081281,3061.101682,3063.117331,3070.138404,3071.133652,3071.158805,3072.154053,3076.076195,3077.096596,3085.112917,3086.133318,3087.128566,3087.153719,3088.148967,3092.071109,3093.09151,3097.185689,3101.107831,3102.128232,3103.148633,3104.143881,3104.169034,3109.086424,3112.160202,3112.185355,3113.180603,3117.102745,3118.123146,3119.143547,3120.163948,3127.159868,3128.155116,3128.180269,3129.175517,3133.097659,3134.11806,3135.138461,3136.158862,3143.154782,3144.175183,3145.170431,3145.195584,3150.112974,3151.133375,3152.153776,3159.149696,3160.170097,3161.190498,3167.128289,3168.14869,3170.202067,3174.149362,3175.14461,3175.169763,3176.165011,3177.185412,3185.201733,3186.196981,3186.222134,3190.144276,3191.139524,3191.164677,3192.159925,3193.180326,3200.176246,3201.196647,3202.217048,3206.13919,3207.159591,3208.154839,3209.17524,3216.17116,3216.196313,3217.191561,3218.211962,3222.134104,3223.154505,3225.170154,3231.170826,3232.166074,3232.191227,3233.186475,3233.211628,3234.206876,3238.129018,3239.149419,3243.243598,3247.16574,3248.186141,3249.181389,3249.206542,3250.20179,3254.123932,3255.144333,3258.218111,3259.238512,3263.160654,3264.181055,3265.201456,3266.196704,3273.217777,3274.213025,3274.238178,3275.233426,3279.155568,3280.175969,3281.19637,3288.19229,3289.212691,3290.207939,3290.233092,3291.22834,3295.150482,3296.170883,3297.191284,3304.187204,3305.207605,3306.228006,3307.223254,3307.248407,3312.165797,3313.186198,3316.259976,3320.182118,3320.207271,3321.202519,3322.22292,3323.243321,3329.181112,3331.259642,3332.25489,3336.177032,3336.202185,3337.197433,3338.217834,3339.238235,3346.234155,3347.254556,3348.249804,3348.274957,3352.197099,3353.192347,3354.212748,3355.233149,3362.229069,3362.254222,3363.24947,3364.269871,3368.192013,3370.207662,3371.228063,3377.228735,3378.223983,3378.249136,3379.244384,3380.264785,3384.186927,3387.222977,3389.276354,3389.301507,3393.223649,3394.218897,3394.24405,3395.239298,3395.264451,3396.259699,3400.181841,3404.27602,3405.296421,3409.218563,3410.238964,3411.234212,3411.259365,3412.254613,3416.176755,3419.275686,3420.270934,3421.291335,3425.213477,3426.233878,3427.254279,3428.249527,3434.250199,3435.2706,3436.265848,3436.291001,3437.286249,3441.208391,3442.228792,3443.249193,3450.245113,3451.265514,3452.260762,3452.285915,3453.281163,3457.203305,3458.223706,3459.244107,3462.317885,3466.240027,3466.26518,3467.260428,3468.280829,3469.276077,3469.30123,3474.21862,3475.239021,3477.292398,3477.317551,3478.312799,3482.234941,3482.260094,3483.255342,3484.275743,3485.296144,3492.292064,3493.287312,3493.312465,3494.307713,3498.229855,3498.255008,3499.250256,3500.270657,3501.291058,3508.286978,3509.307379,3510.302627,3510.32778,3514.249922,3515.24517,3516.265571,3517.285972,3523.286644,3524.281892,3524.307045,3525.302293,3526.322694,3530.244836,3532.260485,3533.280886,3535.334263,3538.261157,3539.281558,3540.276806,3540.301959,3541.297207,3542.317608,3546.23975,3550.333929,3551.329177,3551.35433,3554.256071,3555.276472,3556.27172,3556.296873,3557.292121,3558.312522,3562.234664,3565.308442,3565.333595,3566.328843,3567.349244,3570.250985,3571.271386,3572.291787,3573.287035,3574.307436,3580.308108,3581.303356,3581.328509,3582.323757,3583.344158,3586.245899,3587.2663,3588.286701,3590.30235,3596.303022,3597.29827,3597.323423,3598.318671,3598.343824,3599.339072,3602.240813,3603.261214,3604.281615,3608.375794,3612.297936,3613.318337,3614.313585,3614.338738,3615.333986,3619.256128,3620.276529,3623.350307,3624.370708,3628.29285,3629.313251,3630.333652,3631.3289,3636.271443,3638.349973,3639.345221,3639.370374,3640.365622,3644.287764,3645.308165,3646.328566,3653.324486,3654.344887,3655.340135,3655.365288,3656.360536,3660.282678,3661.303079,3662.32348,3669.3194,3669.344553,3670.339801,3671.360202,3672.35545,3672.380603,3677.297993,3678.318394,3681.392172,3684.319066,3685.314314,3685.339467,3686.334715,3686.359868,3687.355116,3688.375517,3694.313308,3696.391838,3697.387086,3700.31398,3701.309228,3701.334381,3702.329629,3702.354782,3703.35003,3704.370431,3711.366351,3712.386752,3713.382,3713.407153,3716.308894,3717.329295,3718.324543,3718.349696,3719.344944,3720.365345,3726.366017,3727.361265,3727.386418,3728.381666,3729.402067,3732.303808,3733.324209,3734.34461,3735.339858,3736.360259,3741.34053,3742.360931,3743.356179,3743.381332,3744.37658,3745.396981,3748.298722,3749.319123,3750.339524,3752.355173,3754.433703,3757.335444,3758.355845,3759.351093,3759.376246,3760.371494,3760.396647,3761.391895,3764.293636,3765.314037,3766.334438,3769.408216,3770.428617,3773.330358,3774.350759,3775.37116,3776.366408,3776.391561,3777.386809,3781.308951,3782.329352,3784.407882,3785.40313,3786.423531,3789.325272,3790.345673,3791.366074,3792.386475,3793.381723,3799.382395,3800.402796,3801.398044,3801.423197,3802.418445,3805.320186,3806.340587,3807.360988,3808.381389,3815.377309,3815.402462,3816.39771,3817.392958,3817.418111,3818.413359,3822.335501,3823.355902,3824.376303,3827.450081,3830.376975,3831.372223,3831.397376,3832.392624,3833.413025,3834.408273,3834.433426,3839.350816,3840.371217,3842.424594,3842.449747,3843.444995,3846.371889,3847.367137,3847.39229,3848.387538,3849.407939,3850.42834,3857.42426,3858.419508,3858.444661,3859.439909,3862.366803,3863.362051,3863.387204,3864.382452,3865.402853,3866.423254,3872.423926,3873.419174,3874.439575,3875.434823,3875.459976,3878.361717,3879.382118,3880.377366,3881.397767,3882.418168,3887.398439,3888.41884,3889.414088,3889.439241,3890.434489,3891.45489,3894.356631,3895.377032,3897.392681,3898.413082,3903.393353,3904.413754,3905.409002,3905.434155,3906.429403,3907.449804,3910.351545,3911.371946,3915.466125,3916.486526,3919.388267,3920.408668,3921.403916,3921.429069,3922.424317,3923.444718,3926.346459,3927.36686,3930.440638,3930.465791,3931.461039,3932.48144,3935.383181,3936.403582,3937.423983,3938.419231,3939.439632,3943.361774,3945.440304,3946.435552,3946.460705,3947.455953,3948.476354,3951.378095,3952.398496,3953.418897,3955.434546,3961.435218,3962.430466,3962.455619,3963.450867,3963.47602,3964.471268,3967.373009,3968.39341,3969.413811,3973.50799,3976.434884,3977.430132,3977.455285,3978.450533,3979.445781,3979.470934,3980.466182,3984.388324,3985.408725,3988.482503,3989.502904,3992.429798,3993.425046,3993.450199,3994.445447,3995.465848,3996.461096,4001.403639,4003.482169,4004.477417,4004.50257,4005.497818,4008.424712,4009.41996,4009.445113,4010.440361,4011.460762,4018.456682,4018.481835,4019.477083,4020.472331,4020.497484);#for testing
#TMTglycoproteomics: my @unsortedRepIons = (126.12772,127.124761,127.131081,128.128116,128.134436,129.131471,129.137790,130.134825,130.141145,131.138180,131.144500,132.141535,132.147855,133.144890,133.151210,134.148245,134.154565,135.151600,126.054955,127.038970,128.054955,138.054955,144.065519,145.049535,163.0601,168.065519,186.076084,204.086649,243.02643,274.092128,290.08702,292.102693,308.09757,323.224,366.139472,528.192296,657.235438,369.1420,351.1314,531.1943,184.0732);

my $precision = 0.05; # +/- precision in amu, default value: 0.05
my $IgnoreLowMoverZRange = 0; # no deconv or deisotope m/z range below given amu

#----end of PARAMETERS

my $MGF_OUTFILE_NAME;
my $REP_OUTFILE_NAME;
my $MGF_INFILE_NAME;
my $MASS;
my $TITLE;
my $PEPMASS; 
my $PRECURSOR_INTENSITY;
my $CHARGE;
my $RTINSECONDS=0;
my $SCANS=0;
my $NUMBER_MS2SCANS_TOTAL;
my $NUMBER_MS2SCANS_FILTERED;

my @arr1 = ();
my @arr2 = ();
my @v = ();
my $precursor;
my $x;
my $y;
my $i;	

my @RepIons = sort {$a <=> $b} @unsortedRepIons; #sort RepIons list by MoverZ

print "---SugarQBits RepX---\n";
print "parameters:\n";
print "mass precision = +/-$precision amu\n";
print "lower mass exemption < $IgnoreLowMoverZRange amu\n";
print "Reporter Ions:\n";

foreach $x (@RepIons) {
	print $x."\n";
}
print "---   ---\n";

print "INPUT (.mgf) FILE DIRECTORY (full path):>\n";

my $dirname = <>;

chop($dirname);

opendir(DIR, $dirname) or die "Could not open $dirname\n";

my @files = readdir(DIR);

shift @files; #get rid of "."

shift @files; #get rid of ".."

closedir(DIR);

foreach $MGF_INFILE_NAME (@files) {

	$MGF_INFILE_NAME = join ("\\\\", $dirname, $MGF_INFILE_NAME);

	if ($MGF_INFILE_NAME =~ /.MGF/ || $MGF_INFILE_NAME =~ /.mgf/ ){
		
		print "SugarQbits RepX $MGF_INFILE_NAME...";

		open(INFILE,"<$MGF_INFILE_NAME") || die "$MGF_INFILE_NAME not found!\n";
		
		$NUMBER_MS2SCANS_TOTAL = 0; #reset counter
		
		$NUMBER_MS2SCANS_FILTERED = 0;#reset counter

		$MGF_OUTFILE_NAME = ">>".substr ($MGF_INFILE_NAME,0,-4)."_RepX.mgf";

		open (OUTFILE1, $MGF_OUTFILE_NAME);

		$REP_OUTFILE_NAME = ">>".substr ($MGF_INFILE_NAME,0,-4)."_RepIntensities.csv";

		open (OUTFILE2, $REP_OUTFILE_NAME);

		#---write header for csv file

		print OUTFILE2 "MS2 Spectrum Title,Rtime";
				
		for ($x = 0; $x < @RepIons; $x++) { 
		
			print OUTFILE2 ",".$RepIons[$x];		
		
		}
				
		print OUTFILE2 "\n";

		while (<INFILE>){

		chomp;

		@v = split (/=|\s/, $_);
	
		if ($v[0] eq "BEGIN"){
		
			#reset variables and empty arrays of data from previous MS2-spectrum
			
			@arr1 = ();
		
			@arr2 = ();
		
			$NUMBER_MS2SCANS_TOTAL++;
		
			#reset RepIons array arr2
			
			for ($x = 0; $x < @RepIons; $x++) { 
		
				$arr2[$x][0] = $RepIons[$x];
		
				$arr2[$x][1] = 0;	
			
			}
									
		}elsif($v[0] eq "TITLE"){#MGF-MS2-spectrum title
				
			$TITLE = $v[1];	#will truncate msconvert generated "TPP-compatible" spectrum titles, removing all space separated content...
									
		}elsif ($v[0] eq "PEPMASS"){#MGF precursor ion m/z and its intensity
			
			$PEPMASS = $v[1];
			
			if (scalar @v > 2) {
			
				$PRECURSOR_INTENSITY = $v[2];
		
			}else{ #PEAKS generated mgf files do not contain precursor intensity values
		
				$PRECURSOR_INTENSITY = 0;
			
			}
				
		}elsif ($v[0] eq "CHARGE"){#MGF precursor charge state
				
			$CHARGE = substr $v[1], 0, 1; #remove + sign from charge.
				
		}elsif ($v[0] eq "RTINSECONDS"){#MGFclassics RetentionTimeINSECONDS
			
			$RTINSECONDS = $v[1];
			
		}elsif ($v[0] eq "SCANS"){#MGF MS2-spectrum scan number
			
			$SCANS = $v[1]
				
		}elsif ($v[0] eq "END"){
		
			$NUMBER_MS2SCANS_FILTERED++;
		
			print OUTFILE1 "BEGIN IONS\n";
					
			print OUTFILE1 "TITLE=SQbRepX_".$TITLE."\nSCANS=$SCANS\nPEPMASS=$PEPMASS $PRECURSOR_INTENSITY\nCHARGE=$CHARGE+\n";
				
			for ($x = 0 ; $x < @arr1; $x++){
						
				if ($arr1[$x][1] > 0){ #only print value pairs with intensity > 0
							
					print OUTFILE1 "$arr1[$x][0] $arr1[$x][1]\n";

				}
				
			}
				
			print OUTFILE1 "END IONS\n";
			
				
			print OUTFILE2 "TITLE=SQbRepX_".$TITLE.",$RTINSECONDS";
				
			for ($x = 0; $x < @RepIons; $x++) { 
		
				print OUTFILE2 ",".$arr2[$x][1];		
		
			}
				
			print OUTFILE2 "\n";

		}elsif ($v[0] !~ /[a-df-zA-DF-Z]/ && $v[1] !~ /[a-df-zA-DF-Z]/) { #Lines that do not contain letters (but "E" for exponential numbers) are deemed MS2 data pairs
		
			if ($v[0] < $arr2[(@RepIons - 1)][0] + $precision){					
					
				for ($x = 0; $x < @RepIons; $x++) {
					
					if ($v[0] < $arr2[$x][0] + $precision && $v[0] > $arr2[$x][0] - $precision ){

						
						if ($arr2[$x][1] != 0) {

							$arr2[$x][1] = $arr2[$x][1] + $v[1];
														
							$v[1] = 0; #remove RepIons from MS2 spectrum by setting Intensity value to 0
					
						
						}else{
							
							$arr2[$x][1] = $v[1];
							
							$v[1] = 0; #still remove RepIons from MS2 spectrum by setting Intensity value to 0?
						
						}
					
					}

				}
					
			}
					
			push @arr1, [$v[0], $v[1]];
	
		}else{
		
			print "dont know what to do with: $v[0]-$v[1]\n";
		
		}	
		
	}
	
	close OUTFILE2;

	close OUTFILE1;

	close INFILE;
	
	print "done!\n($NUMBER_MS2SCANS_FILTERED RepXFiltered/$NUMBER_MS2SCANS_TOTAL total)\n";

}

}