#!/usr/bin/env perl
use warnings;
use strict;
use FindBin;
use lib "$FindBin::RealBin/../perl5";
###LINE_FOR_BREW_CONDA###
use Snippy::Version;
use Bio::SeqIO;
use File::Basename;

# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
# Globals

my $VERSION = Snippy::Version->version;
my $EXE = $FindBin::RealScript;
my $URL = "http://github.com/tseemann/snippy";
my @CMDLINE = (basename($EXE), @ARGV);

# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
# Options

my(@Options, $debug);
my $to = 'N';
setOptions();

length($to)==1 or err("--to must be a single character, not '$to'");

my $in  = Bio::SeqIO->new(-fh=>\*ARGV,   -format=>'fasta', -alphabet=>'dna');
my $out = Bio::SeqIO->new(-fh=>\*STDOUT, -format=>'fasta', -alphabet=>'dna');
while (my $seq = $in->next_seq) {
  my $dna = $seq->seq;
  $dna = uc($dna);
  $dna =~ s/[^ACGTN-]/$to/g;
  length($dna)==$seq->length or err("Conversion produced mismatched DNA lengths for ".$seq->id);
  $seq->seq($dna);
  $out->write_seq($seq);
}

#----------------------------------------------------------------------
sub msg { print STDERR "@_\n";}
sub wrn { msg("NOTICE:", @_); }
sub err { msg("ERROR:", @_); exit(2); }

sub show_version {
  print "$EXE $VERSION\n";
  exit(0);
}

#----------------------------------------------------------------------
# Option setting routines

sub setOptions {
  use Getopt::Long;

  @Options = (
    {OPT=>"help!",       VAR=>\&usage,                        DESC=>"This help"},
    {OPT=>"version!",    VAR=>\&show_version,                 DESC=>"Print version and exit"},
    {OPT=>"debug!",      VAR=>\$debug,      DEFAULT=>0,       DESC=>"Output verbose debug info"},
    {OPT=>"to=s",         VAR=>\$to,      DEFAULT=>'N',       DESC=>"Replacement char"},
  );

  (!@ARGV) && (usage());

  &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage();

  # Now setup default values.
  foreach (@Options) {
    if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
      ${$_->{VAR}} = $_->{DEFAULT};
    }
  }
}

sub usage {
  select STDERR;
  print "SYNOPSIS\n  Replace non-[AGTCN-] chars with '$to'\n";
  print "USAGE\n";
  print "  $EXE [options] core.full.aln > gubbins.aln\n";
  print "OPTIONS\n";
  foreach (@Options) {
    printf "  --%-11s %s%s.\n",$_->{OPT},$_->{DESC},
           defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
  }
  print "HOME\n  $URL\n";
  exit(1);
}
 
#----------------------------------------------------------------------