#!/opt/miniconda/envs/bioconda/conda-bld/meme_1682225782810/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/bin/perl
=head1 NAME

dreme_xml_to_html - Make a DREME HTML output from a DREME XML output.

=head1 SYNOPSIS

dreme_xml_to_html <DREME XML file> <DREME HTML file>
=cut

use strict;
use warnings;

use Cwd qw(abs_path);
use Fcntl qw(O_CREAT O_RDONLY O_WRONLY O_TRUNC SEEK_SET);
use File::Basename qw(fileparse);
use File::Spec::Functions qw(tmpdir);
use File::Temp qw(tempfile);
use Getopt::Long;
use Pod::Usage;
use XML::Parser::Expat;

use lib '/opt/miniconda/envs/bioconda/conda-bld/meme_1682225782810/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/perl';

my $etc_dir;
my $temp_dir;
my $scripts_dir;

#
# initialise the global constants
# 
sub initialise {
  # setup etc dir
  $etc_dir = defined($ENV{MEME_ETC_DIR}) ? $ENV{MEME_ETC_DIR} : '/opt/miniconda/envs/bioconda/conda-bld/meme_1682225782810/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/etc';
  # setup temporary directory
  $temp_dir = '';
  # use the perl default if none is supplied or the replace fails
  $temp_dir = tmpdir() if ($temp_dir eq '' || $temp_dir =~ m/^\@TMP[_]DIR\@$/);

  # find the location of the script
  my $script_name;
  ($script_name, $scripts_dir) = fileparse(__FILE__);
  $scripts_dir = abs_path($scripts_dir);

  # add script location to search path
  unshift(@INC, $scripts_dir);

  require Alphabet;
  require DremeSAX;
}

sub arguments {
  # Set Option Defaults
  my $options = {XML_PATH => undef, TXT_PATH => undef};
  # General Options
  my $help = 0; # FALSE
  my @errors = ();
  my @dbs = ();

  # get the options from the arguments
  my $options_success = 0; # FALSE
  # redirect stderr to a temp file so we can get the error message from GetOptions
  my $olderr;
  my $tmperr = tempfile('GetOptions_XXXXXXXXXX', DIR => $temp_dir, UNLINK => 1);
  open($olderr, ">&STDERR") or die("Can't dup STDERR: $!");
  open(STDERR, '>&', $tmperr) or die("Can't redirect STDERR to temp file: $!");
  # parse options
  $options_success = GetOptions(
    'help|?'          => \$help,
  );
  ($options->{XML_PATH}, $options->{TXT_PATH}) = @ARGV;
  # display help
  pod2usage(1) if $help;
  # reset STDERR
  open(STDERR, ">&", $olderr) or die("Can't reset STDERR: $!");
  # read argument parsing errors
  seek($tmperr, 0, SEEK_SET);
  while (<$tmperr>) {chomp; push(@errors, $_);}
  close($tmperr);
  # check source XML file
  unless (defined($options->{XML_PATH})) {
    push(@errors, "No DREME XML file specified");
  } elsif (not -e $options->{XML_PATH}) {
    push(@errors, "The DREME XML file specified does not exist");
  }
  unless (defined($options->{TXT_PATH})) {
    push(@errors, "No output file specified");
  }
  # print errors
  foreach my $error (@errors) {
    print STDERR $error, "\n";
  }
  pod2usage(2) if @errors;
  # return options
  return $options;
}

sub start_dreme {
  my ($info, $vmajor, $vminor, $vpatch, $release_date) = @_;
  $info->{version} = "$vmajor.$vminor.$vpatch";
  my $fh = $info->{fh};
  print $fh "# DREME ", $info->{version}, "\n";
}

sub end_dreme {
  my ($info) = @_;
}

sub start_model {
  my ($info) = @_;
  $info->{model} = {};
}

sub end_model {
  my ($info) = @_;
}

sub handle_command_line {
  my ($info, $command_line) = @_;
  my $fh = $info->{fh};
  print $fh "#     command: $command_line\n";
}

sub handle_positives {
  my ($info, $name, $count, $file, $last_mod_date) = @_;
  my $fh = $info->{fh};
  print $fh "#   positives: $count from $file ($last_mod_date)\n";
}

sub handle_negatives {
  my ($info, $name, $count, $from, $file, $last_mod_date) = @_;
  my $fh = $info->{fh};
  print $fh "#   negatives: $count from ";
  if ($from eq 'shuffled') {
    print $fh "shuffled positives\n";
  } else {
    print $fh "$file ($last_mod_date)\n";
  }
}

sub handle_alphabet {
  my ($info, $alphabet) = @_;
  $info->{alph} = $alphabet;
}

sub handle_strands {
  my ($info, $strands) = @_;
  $info->{model}->{strands} = $strands;
}

sub handle_background {
  my ($info, @probs) = @_;
  $info->{model}->{background} = [@probs];
}

sub handle_stop {
  my ($info, $evalue, $count, $time) = @_;
}

sub handle_ngen {
  my ($info, $ngen) = @_;
}

sub handle_add_pv_thresh {
  my ($info, $pv_thresh) = @_;
}

sub handle_seed {
  my ($info, $seed) = @_;
}

sub handle_host {
  my ($info, $host) = @_;
  my $fh = $info->{fh};
  print $fh "#        host: $host\n";
}

sub handle_when {
  my ($info, $when) = @_;
  my $fh = $info->{fh};
  print $fh "#        when: $when\n";
}

sub handle_description {
  my ($info, $description) = @_;
  my $fh = $info->{fh};
  print $fh "# description: ", join("\n#            : ", split(/\n/, $description)), "\n";
}

sub start_motifs {
  my ($info) = @_;
  my $fh = $info->{fh};
  print $fh "\nMEME version ", $info->{version}, "\n\n";
  my $alph = $info->{alph};
  print $fh $alph->to_text();
  if ($alph->has_complement()) {
    if ($info->{model}->{strands} eq 'both') {
      print $fh "\nstrands: + -\n";
    } else {
      print $fh "\nstrands: +\n";
    }
  }
  print $fh "\nBackground letter frequencies (from dataset):\n";
  my $i;
  for ($i = 0; $i < $alph->size_core(); $i++) {
    print $fh ' ' unless $i == 0;
    print $fh $alph->char($i), ' ', $info->{model}->{background}->[$i];
  }
  print $fh "\n";
}

sub end_motifs {
  my ($info) = @_;
}

sub start_motif {
  my ($info, $id, $seq, $len, $nsites, $p, $n, $pvalue, $evalue, $unerased_evalue) = @_;
  my $fh = $info->{fh};
  print $fh "\n\nMOTIF $seq DREME\n\n";
  my $alen = $info->{alph}->size_core();
  $info->{pssm} = "letter-probability matrix: alength= $alen w= $len nsites= $nsites E= $evalue\n";
  if ($info->{alph}->has_complement()) {
    $info->{words} = "#             Word    RC Word        Pos        Neg    P-value    E-value\n";
    $info->{words} .= sprintf("# BEST  %10s %10s %10s %10s %10s %10s\n", $seq, $info->{alph}->rc_seq($seq), $p, $n, $pvalue, $evalue);
  } else {
    $info->{words} = "#             Word        Pos        Neg    P-value    E-value\n";
    $info->{words} .= sprintf("# BEST  %10s %10s %10s %10s %10s\n", $seq, $p, $n, $pvalue, $evalue);
  }
}

sub end_motif {
  my ($info) = @_;
  my $fh = $info->{fh};
  print $fh $info->{words}, "\n";
  print $fh $info->{pssm};
}

sub handle_pos {
  my ($info, @probs) = @_;
  $info->{pssm} .= join(" ", @probs) . "\n";
}

sub handle_match {
  my ($info, $seq, $p, $n, $pvalue, $evalue) = @_;
  if ($info->{alph}->has_complement()) {
    $info->{words} .= sprintf("#       %10s %10s %10s %10s %10s %10s\n", $seq, $info->{alph}->rc_seq($seq), $p, $n, $pvalue, $evalue);
  } else {
    $info->{words} .= sprintf("#       %10s %10s %10s %10s %10s\n", $seq, $p, $n, $pvalue, $evalue);
  }
}

sub handle_run_time {
  my ($info, $cpu, $real, $stop) = @_;
  my $fh = $info->{fh};
  print $fh "\n\n# Stopping reason: ";
  if ($stop eq 'evalue') {
    print $fh "E-value threshold exceeded\n";
  } elsif ($stop eq 'count') {
    print $fh "target motif count reached\n";
  } elsif ($stop eq 'time') {
    print $fh "maximum running time reached\n";
  }
  print $fh "#    Running time: $real seconds\n";
}

sub transform_data {
  my ($opts, $out_fh) = @_;
  my $info = {fh => $out_fh};

  my $sax = new DremeSAX($info,
    start_dreme => \&start_dreme,
    end_dreme=> \&end_dreme,
    start_model => \&start_model,
    end_model => \&end_model,
    handle_command_line => \&handle_command_line,
    handle_positives => \&handle_positives,
    handle_negatives => \&handle_negatives,
    handle_alphabet => \&handle_alphabet,
    handle_strands => \&handle_strands,
    handle_background => \&handle_background,
    handle_stop => \&handle_stop,
    handle_ngen => \&handle_ngen,
    handle_add_pv_thresh => \&handle_add_pv_thresh,
    handle_seed => \&handle_seed,
    handle_host => \&handle_host,
    handle_when => \&handle_when,
    handle_description => \&handle_description,
    start_motifs => \&start_motifs,
    end_motifs => \&end_motifs,
    start_motif => \&start_motif,
    end_motif => \&end_motif,
    handle_pos => \&handle_pos,
    handle_match => \&handle_match,
    handle_run_time => \&handle_run_time
  );
  my $fh;
  sysopen($fh, $opts->{XML_PATH}, O_RDONLY) or die("Failed to open file \"$opts->{XML_PATH}\"\n");
  while (<$fh>) {
    $sax->parse_more($_);
    if ($sax->has_errors()) {
      die("Failed to write HTML output due to errors processing the XML:\n" . join("\n", $sax->get_errors()));
    }
  }
  $sax->parse_done();
  if ($sax->has_errors()) {
    die("Failed to write HTML output due to errors processing the XML:\n" . join("\n", $sax->get_errors()));
  }  
}

sub main {
  &initialise();
  my $opts = &arguments();
  # open the output file
  my $fh;
  sysopen($fh, $opts->{TXT_PATH}, O_WRONLY | O_CREAT | O_TRUNC) or die("Failed to open file \"$opts->{TXT_PATH}\" for writing\n");
  # transform the XML into text
  &transform_data($opts, $fh);
}

&main();
1;

