#!/usr/bin/perl -w

# usage : sm_clones_meta1.pl
#sarah maman - 10 dec 2013 - Mis en place pour le traitement des clones metagenomiques

use strict;
use File::Basename;


my $output = $ARGV[0];
my $inputs = @ARGV[1..$#ARGV];
my $MASQUAGEVECTEUR = '/usr/local/bioinfo/bin/cross_match';
my $cmd = '';

#cross_match Pyrocleaner/RL1/Formation.RL1.decontaminated.clean.fasta.cap.contigs Vector/pCC1FOS.fasta -minmatch 9 -minscore 30 -screen > cap-contigs.fasta


foreach my $file (@ARGV[1..$#ARGV]){
	$cmd = "(sh $MASQUAGEVECTEUR @ARGV[1..$#ARGV] $fasta -minmatch 9 -minscore 30 -screen > cap-contigs) >& ./cross_match.log 2>&1";
	system $cmd;
}

#EN ENTREE :
#Query file(s):  Pyrocleaner/RL1/Formation.RL1.decontaminated.clean.fasta.cap.contigs
#Subject file(s):   Vector/pCC1FOS.fasta


#EN SORTIE :
#Log file: Pyrocleaner/RL1/Formation.RL1.decontaminated.clean.fasta.cap.contigs.log
#cap-contigs (a la racine, nom donné par le script)
#Pyrocleaner/RL1/Formation.RL1.decontaminated.clean.fasta.cap.contigs.screen

	
if (! -e "cap-contigs")
{
print STDERR "Echec lors de la generation du fichier cap-contigs.fasta\n";
}
else
{
$cmd = "(cp -a cap-contigs.fasta $output_fasta) >& ./cpcross1.log 2>&1";
system $cmd;
}