#!/usr/bin/perl -w
# Script to run BLASTN on a FASTA files containing split contigs, 
# creating the sequence fragments to be BLASTed if needed

use Critica;

$scriptname=getScriptName();

@files=realArguments(@ARGV);
(@files==1) || die ("$scriptname [-db=] fasta-file\n");
$filename=pop(@files);

$blastn="blastn";
if (defined($x = $ENV{"CRITICA_BLASTN"}))  { 
  $blastn = $x;
}
$parameters="-warnings -nogaps E=1e-4 E2=1e-4 ";
if (defined($x = $ENV{"CRITICA_BLASTPARM"}))  { 
  $parameters = $x;
}
$db="gb";
if (defined($x = $ENV{"CRITICA_BLASTDB"}))  { 
  $db = $x;
}


@flags=flagArguments(@ARGV);
foreach $flag (@flags) {
  if (index($flag,"-db=")>-1) {
    (undef,$db)=split("=",$flag);
  }
  else {
    die("$scriptname: flag $flag not understood.\n");
  }
}


$dirname=getPrefixName($filename)."dir";

if (!-e("$dirname")) {  
 createBlastFragments($dirname,$filename, 3000, 100);
}

opendir(DIR,$dirname) || die("Can't find $dirname! Aborting\n");
@files=readdir(DIR);
closedir(DIR);

shift(@files);shift(@files);
foreach $file (@files) 
{
  $f=$dirname."/".$file;
  $fq=quotemeta($f);
  $n="$blastn $db $fq $parameters";
  @output = `$n`;
  foreach $line (@output)
  {
      print $line;
  }
  unlink $f;
}
rmdir($dirname);