#!/usr/bin/perl

####################################
#
# SeparateElandReads.pl -f Eland-file -o output-path
#
# reads Eland-files line by line
# writes line to file contig_name.eland
# if file exits: appends
# if file does not exits: creates
# known bugs: does not delete files in output folder before writing! DO IT MANUALLY!
#####################################

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

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

use vars qw( $opt_f $opt_o);

# Command line parsing 
#
getopts('f:o:');
#
# Handle missing / at path end:
#
if ($opt_o=~/\/$/)
   {$opt_o=$opt_o}
   else
   {$opt_o=$opt_o."/"}
   
print "Reading file: ".$opt_f."\n";
print "Writing to output directory: ".$opt_o."\n";
#replace Mac and PC CRLF by UNIX LF
system ("perl -pi -e 's/\r/\n/g' $opt_f");
#
# Read input file and write each line in an array cell
#
open($FILE,$opt_f) || croak(sprintf("Cannot open file \"%s\"",$opt_f));
while ( <$FILE> ) {
    chomp;
    s/\ /_/g;
    if ( /^>(\S+)/) 
         {
         push(@elandline,$_);
         $linesread++;
         } 
       else 
         {
         #do nothing
         }
       }
close($FILE) || croak(sprintf("Cannot close open file \"%s\"",$opt_f));
print "File read. ".$linesread." lines processed."."\n";
#
# Loop through array and write into individual files
#
for $i (0 .. $#elandline)
         {
         $elandlinenumber=$elandlinenumber+1;
         @temp = ();
         @temp=split('\t',$elandline[$i]);
		 $contigname=$temp[6];
         $outfile = $opt_o . $contigname . ".eland";
open($FILE,">>".$outfile) || croak(sprintf("Cannot open file \"%s\"",$outfile));
print $FILE (($elandline[$i])."\n");
         }
close ($FILE);
print "Finished. ".$elandlinenumber." sequences processed."."\n";