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

my $file = $ARGV[0];
my @file = split(/\./,$file);
my $name = $file[0];

my $splitcolumn = $ARGV[1]; # splitcolumn value is 2

if ($#ARGV != 1 ) 
{
    print "Usage: Program_name filename column_number\n";
    exit;
}

open (X, ">", $name."_detailed_info.txt");
open (Y, ">", "temp_".$name."_concatenate.dat");
open (ERR, ">",$name."_log.file");
my @alphabets = ("A".."H"); my @numbers = (1..12);
my $cellno = 1; my $count=1; my $alphacounter=0; 
my $numcounter = 0; my $targetlen = 19;
my $errseq=1; my $errlen =1; my @seq;
#print X "#Name\tTarget_Seq(5'->3')\tTarget_len\tTarget_GC%\tShort_mRNA(5'->3')\tSense_Strand\tSS_len\tSS_GC%\tAntiSense_Strand(5'->3')\tAnit_Sense\tAS_len\n";
open (A, "<","$file") or die "Could not open the file, $!";
while(my $line = <A>)
{
    chomp $line;
		if ($line =~/^\s*$/)
		{next;}
    my @temp = split(/\s/,$line);
#    my $seq = uc($temp[2]); #Target mRNA, length 19 bp
    my $seq = uc($temp[$splitcolumn]); #Target mRNA, length 19 bp
		my @tempseq = split (//,$seq);
		foreach my $tempseq(@tempseq)
		{
			if ($tempseq !~/[ATGC]/ig)
			{
		    print ERR "Error: Target sequence # $errseq: [".$seq."] has bases other than ATGC.\n";
				next;
			}
		}
				
    my $lenseq = length($seq);
		if ($lenseq < $targetlen || $lenseq > $targetlen)
		{
			print ERR "Error: Target sequence # $errseq: [".$seq."] is of ".length($seq)."-bp.\n";
			next;
		}
		$errseq++;
		
    my $a = ($seq=~tr/A//);
    my $t = ($seq=~tr/T//);
    my $g = ($seq=~tr/G//);
    my $c = ($seq=~tr/C//);
    my $GCper = sprintf ("%.2f", (($g+$c)/$lenseq)*100);
    my $ATper = sprintf ("%.2f", (($a+$t)/$lenseq)*100);

    my $mrna = $seq;
    $mrna =~ s/T/U/g;
    $mrna =~ /\w{3}(.*)\w{1}/;
    my $shortmrna = $1; #Short mRNA, first 3 and last 1 base removed
#   print "$shortmrna\n";
    my $lenshortmrna = length ($shortmrna);
    my $aa = ($shortmrna=~tr/A//);
    my $uu = ($shortmrna=~tr/U//);
    my $gg = ($shortmrna=~tr/G//);
    my $cc = ($shortmrna=~tr/C//);
    my $GCCper = sprintf ("%.2f", (($gg+$cc)/$lenshortmrna)*100);
    my $ATTper = sprintf ("%.2f", (($aa+$uu)/$lenshortmrna)*100);

    my $antisense = $seq;
    $antisense =~ tr/ATGCatgc/UACGuacg/;
    my $reverse = "AA".reverse($antisense); #Antisense strand made from target mRNA, added two A's at beginning.
#   print "$reverse\n";
    my $lenreverse = length($reverse);
    print X "$name$count\t$seq\t$lenseq\t$GCper\t$shortmrna\tSS\t$lenshortmrna\t$GCCper\t$reverse\tAS\t$lenreverse\n"; #Detailed information print
    print Y "$name$count\tSS\t$shortmrna\n"; #tempfile print
    print Y "$name$count\tAS\t$reverse\n"; #tempfile print 
    $count++;		
}
close (A); close (X); close (Y);