#!/usr/bin/perl
# Usage - ESTsearch <fasta filename> <directory to put files>

$ext = $ARGV[0];

$input = $ext;
$input.="EST";
$match=$ext;
open(INPUT, $input)  || die "Unable to open $input\n";

$dir = "Clus";
$tmp_dir="tmp";
mkdir("$tmp_dir",0775);
mkdir("$dir",0775);
print "Made directory $dir\n";

while(<INPUT>) {
	if(/>/) {
		chop;
		$_ =~ /($match\d\d\d\d\d)$/;
      		$filename = $1;
		print "$match processing $filename\n";
		open(OUTFILE, ">>$tmp_dir/$filename") || die "Can't open $filename\n";
		print OUTFILE "$_\n";
		next;
	}
	print OUTFILE $_ unless(/^>/);
	if (/^>/) {
		close OUTFILE;
	}
}
close OUTFILE;
close INPUT;

opendir(DIR, "tmp");
while (defined($file=readdir(DIR))) {
$no_seqs=0;
if($file =~ /^$ext/) {
open(INPUT, "<$tmp_dir/$file");
while(<INPUT>) {
 if (/^>/) { $no_seqs++ }
    }
 close INPUT;
 if($no_seqs==1) {
 system("cat $tmp_dir/$file >> $dir/singletons.fasta");
 system("rm $tmp_dir/$file");
    }
 else {
 system("mv $tmp_dir/$file $dir/$file");
  }
 }
}