#!/usr/local/public/bin/perl
$VERSION = 0.1;
###########################################################
# GGsnp_update.pl
#
# Read a singlet file and all contig files from a directory
# Make a file containing all sequence in fasta format
# 
# Laurence Amilhat le 21 Février  2003
# UMR INRA UBP-ASP
# Clermont-ferrand France
###########################################################

use strict;
use vars qw($opt_h);
use Getopt::Std;

getopts('h');

###########################################################
# Recupere les noms de fichier et de repertoire
###########################################################
print "Enter singlet file:\n";
my $FILE_S=<STDIN>;
chomp $FILE_S;

print "Enter contig directory:\n";
my $DIRECT=<STDIN>;
chomp $DIRECT;

open (OUT, "> GGupdate.tfa");

###########################################################
# Main
###########################################################

# convert not ATGC caracters by N in the singlet file
open (SINGLET, "$FILE_S") || die "cannot find $FILE_S\n";
my $id;
my $sequence;
my $seq_fasta;

while (<SINGLET>)
{
	chomp;
	if (/^>/)
	{
		$id=$_;
		print OUT "$id\n";
	}
	else
	{
		$sequence=convert($_);
		print OUT "$sequence\n";
	}
}
close (SINGLET);


# read each file in the contig directory

open (CONTIGDIR,"ls -R $DIRECT |")|| die "cannot find $DIRECT\n";

my $dir;

while (<CONTIGDIR>)
{
	if (/^(\S+):$/)
	{
		$dir=$1;
	}
	elsif (/^(\S+)$/)
	{
		my $contig_file=$1;
		open (CONTIG, "$dir/$contig_file") || die "cannot find $contig_file\n";
		undef $/;
		print " processing $dir/$contig_file \n";
		my $contig=<CONTIG>;
		$/="\n";
		if ($contig =~ /(^>contig.*\n)(^(?!>).*\n)*/gm)
		{
			my $name=$1;
			my $seq=convert($2);
			$/="\n";
			chomp ($name,$seq);
			my $seq_fasta= fasta(name=>$name,seq=>$seq);
			print OUT $seq_fasta;
		}
		close(CONTIG);
	}
}
close (OUT);
##########################################################
# Subroutines
##########################################################

# convert non ATGC letters to N
sub convert {
	my $ligne=shift @_;
	$ligne =~ tr/[a-z]/[A-Z]/;
	$ligne =~ tr/[ATGCN\n]/N/c;
	return $ligne;
}


# print a sequence in fasta format
sub fasta {
	my %param=(
		seq=>"",
		name=>"",
		@_);
	my $fasta=$param{name}."\n";
	my $line;
	my $i=0;
	my $COL=60;
	
	while($line=substr($param{seq},$i,$COL))
	{
		$i+=$COL;
		$fasta .= $line."\n";
	}
	return $fasta;
}


# Help 
sub help {
my $message = shift;
print "\n$message\n";
print <<EOF;

GGsnp_update.pl : Read a singlet file and all contig files from a directory
		  Make a file containing all sequence in fasta format
		
Usage: GGsnp_update.pl
	
Out: GGupdate.tfa

EOF
exit(0);
}

1;