#!/usr/bin/perl
#Naga_betrapally_6_3_16
use strict;
use warnings;
use Cwd;
use FileHandle;
my $name;                         														# Naming of variables, remembers the name of the file
my $cwd = getcwd();              														#Takes in the current directory of files
my $opendir = "$cwd";           														#Used to open the current directory and remembers the location
opendir (DIR, $opendir) or die $!;          											#Open directory command
my @directory = readdir DIR;     														#Grabbing all the fas files stored in the location
my $scalar = scalar(@directory);                										#Counting the number of files and printing it in the next line
#print "The number of sample files in this folder: $scalar \n";
# for (my $i=0; $i<scalar(@directory); $i++){
# $name = "$directory[$i]";
# print "The file read in: $name\n";
# my $digits = substr $name, 0, 4;                  									#Grabbing the first 4 characters to name the sample run for MEGA
# my $tmp = "$opendir/$directory[$i]";

# }

for(my$i=0;$i<@directory;$i++){
print $directory[$i];
&average($directory[$i]);
}

 #average(@directory);

sub average {
my $header;
my @array_lines;
my $n=0;
my $filename=@_; 																			#Takes in the sequence file from the user input with the year in the header
my @average_array;
my $sum =0;
my $avarage;
	 next if($filename =~ /^\.$/);
     next if($filename =~ /^\.\.$/);
open (FILE,$filename) or die "No input file provided or the input file does not exist in the path, '$_' $!";
print "$filename\n";
while (my $file = <FILE>){
chomp $file;
if ($file =~/^Name/){
$header = $file;
}
else{
$array_lines[$n] = $file;  
chop $array_lines[$n];
$n++;
}
}					
for(my $i=0;$i<@array_lines;$i++){
my @tmp = split(/\t/,($array_lines[$i]));
#print $tmp[3];
push @average_array, $tmp[3];
my $scalar = scalar(@average_array);
#print $scalar;
}	
foreach (@average_array){
	#print "$_\n";
	my $tmp = $_;
	$tmp =~ s/,//;
	#print "$tmp\n";
	$sum = $sum+$tmp;
	}	
#print "The sum of all the mapping is $sum\n";
$avarage = $sum/11;
#print "THe average of the mapping is $avarage\n";
close (FILE);
}

##</code><code>##

Name	Consensus length	Total read count	Average coverage	Reference sequence	Reference length
NSP4-E1 mapping	750	227760	64,516.84	NSP4-E1	750
VP7-G3 mapping	1062	303758	63,062.33	VP7-G3	1062
Rotarix-VP6 mapping	1356	161491	26,020.50	Rotarix-VP6	1356
Rotarix-NSP1 mapping	1559	114394	16,077.21	Rotarix-NSP1	1568
NSP2-N1 mapping	1059	80424	16,178.61	NSP2-N1	1058
NSP5-H1 mapping	664	75269	23,943.71	NSP5-H1	663
VP1-R1 mapping	3302	69677	4,542.15	VP1-R1	3302
VP2-C1 mapping	2717	149312	11,987.00	VP2-C1	2717
VP3-M1 mapping	2591	31795	2,632.39	VP3-M1	2591
RotaTeq-WI79-4-VP4 mapping	2359	78305	7,223.08	RotaTeq-WI79-4-VP4	2359
NSP3-T1 mapping	1074	173210	34,910.87	NSP3-T1	1074