#!/usr/bin/env perl
# -*- perl -*-

=head1 mlocarna_nnames

mlocarna_nnames

=head1 SYNOPSIS

mlocarna_nnames <fasta-file>

=head1 DESCRIPTION

Normalize the names in the fasta file in the way of mlocarna. mlocarna uses the normalized names in file names of sequence specific files, e.g. in sub-direcory input of its result directory.

=head1 OPTIONS

=over 8

=item  B<--help>

Brief help message

=item  B<--man>                         

Full documentation

=back

=cut

use warnings;
use strict;
use FindBin;
use lib "$FindBin::Bin/../lib/perl";

use MLocarna;
use MLocarna::SparseMatrix;
use MLocarna::Trees;
use MLocarna::MatchProbs;
use MLocarna::Aux;


##------------------------------------------------------------
## options

use Getopt::Long;
use Pod::Usage;

my $help;
my $man;
my $quiet;
my $verbose;


GetOptions(	   
    "verbose" => \$verbose,
    "quiet" => \$quiet,   
    "help"=> \$help,
    "man" => \$man
    ) || pod2usage(2);

pod2usage(1) if $help;
pod2usage(-exitstatus => 0, -verbose => 2) if $man;

my $seqs_file = $ARGV[0];
if (!defined($seqs_file)) {
    print STDERR "Please specify an input file.\n";
    pod2usage(-exitstatus => -1, -verbose => 1);
}


## ------------------------------------------------------------
## main part

my $seqs = read_fasta($seqs_file); ## input sequences
register_normalized_seqnames($seqs); ## register normalized names for them that can be used as filenames
print_normalized_sequence_names_hash();

## ------------------------------------------------------------


