#!/usr/bin/perl

####################################
#
# AnalyzeElandFiles.pl -i input-path with Eland files (*.eland)
#
# reads Eland-files line by line
# count number of line = number of hits
# get value of column nr.11 = scaffold name
#####################################

use diagnostics;
use strict;
use Carp;
use FileHandle;
use File::Path;
use File::Basename;
use Getopt::Std;

my @peakline         = ();
my @temp = ();
my @score = ();
my @peakfile = ();
my $peakfile = "";
my $FILE              = FileHandle->new();
my $seq = "";
my $num = 0;
my $i;
my $outfile = "";
my $contigname = "";
my $j;
my $seqname = "";
my $peaklinenumber = 0;
my $linesread = 0;
my $inputdir = "";
$| = 1;                          #print immediately

use vars qw( $opt_i );

# Command line parsing 
#
getopts('i:');
#
# Handle missing / at path end:
#
if ($opt_i=~/\/$/)
   {$opt_i=$opt_i}
   else
   {$opt_i=$opt_i."/"}
   
print "Reading input directory: ".$opt_i."\n";

print "scaffold\thits\n";

$inputdir = "$opt_i"."\*\.eland";
@peakfile = glob($inputdir);
foreach $peakfile (@peakfile) 
        {
#
# Read input file and write each line in an array cell
#
$linesread=0;
@peakline = ();
open($FILE,$peakfile) || croak(sprintf("Cannot open file \"%s\"",$peakfile));
while ( <$FILE> ) 
      {
       chomp;
       push(@peakline,$_);
       $linesread++;
       }
close($FILE) || croak(sprintf("Cannot close open file \"%s\"",$peakfile));
#
# Loop through array
#
$peaklinenumber=0;
@temp = ();
$i = 0;
for $i (0 .. $#peakline)
         {
         $peaklinenumber++;
         @temp = ();
         @temp=split('\t',$peakline[$i]);
         }
print "$temp[11]\t$peaklinenumber\n";
}