#!/usr/bin/perl -w
use strict;

#############################################
# Authors: Marta Massanella, Ingrid Pallās  #
# 	   Charles Chapple & Josep Abril    #
# Date: March 2005                          #
#############################################

my %positions;
my ($name, $seq); 


open (SEQ , "$ARGV[0]") || die("no file : $!\n");
while(<SEQ>)
{
    next if />/;
    $seq = $_;
    chomp $seq;
}
close(SEQ);


open(SNP, "$ARGV[1]") || die("no file : $!\n");

while(<SNP>)
{
    next unless /Sequence/;

    $_ =~ />(.*?)\s.*?:\s+(.*)$/ || die("no match $_\n");
    $name = $1;
    my @snps = split(/\s+/, $2);
   
    my @ch;
    foreach my $snp (@snps)
    { 
	$snp =~ /(\d+)(.*)/;
	my @c = split (//, $2);
	@c = ($1, @c);
	push @ch, [@c];
    }

    $positions{$name} = [@ch];
}
close(SNP);

my @keys = keys(%positions);

foreach my $sequence_name (@keys)
{
    print "=============$sequence_name============\n";
    my @array = @{$positions{$sequence_name}};

    my @seqs = &makeseqs($seq, @array);

    my $slen = length $seq;
    $slen = "." x $slen;
    map { substr($slen,$_->[0],1) = '|' } @array;

    print "$slen\n";
    my $i = 0;
    map {print ">$i\n$_\n"; $i++} @seqs;

}



sub makeseqs
{
 my ($seq, $array, @P) = @_;
 

 return $seq unless defined $array;

my ($pos, @changes) = @$array;

 my @out = ();
 
 foreach my $nuc (@changes)
 {
     my $temp = ($seq, $pos);
     
    
     if ($nuc eq '-')
     {
	 substr($seq, $pos, 1) = ''; 
     }
     else
     {
	 substr($seq, $pos, 1) = $nuc;
     }
#     print $seq, "\n";

     push @out, makeseqs($seq, @P);	 
 }
 return @out;


}