#!/usr/bin/perl -w

use strict;
use warnings;

use Cwd qw(abs_path);
use Getopt::Long;
use File::Basename;
use File::Copy;
use File::Path qw(mkpath);
use File::Spec::Functions qw(catfile);
use Pod::Usage;

=head1 NAME

meme-rename - copy & rename files so they can be stored together avoiding naming conflicts.

=head1 SYNOPSIS

meme-rename [options] <dir>+

  Options
    <dir>+          full path of MEME Suite program output directory
    [-d <dest>]     destination directory; default: working directory 
    [-h]            print this message

    Copy HTML files from MEME Suite programs to files with distinct names to 
    make it easier to share them:
            <dest>/<program>.<last_dir>[.<arg_order_num>].html
    where <last_dir> is the last directory on the path, and <program> is the
    name of the MEME Suite program. If the <program>.<last_dir> combination is
    not unique then a number based on the argument order is added.

=cut

sub cp {
  my ($from, $to) = @_;
  print STDERR "Copying $from to $to\n";
  copy($from, $to);
}

sub main {
  # configuration
  my $dest = ".";
  my $help = 0; # FALSE
  GetOptions(
    "destination=s" => \$dest,
    "help|?" => \$help 
  ) or pod2usage(2);
  my @dirs = @ARGV;

  # display help
  pod2usage(1) if $help;

  # check source directories are provided
  pod2usage("No directories specified") unless (@dirs);

  # check destination is ok
  if (-e $dest) {
    die("The destination is not a writable directory.") unless (-d $dest && -w $dest);
  } else {
    mkpath($dest, {verbose => 1});
  }

  # store map of destination file names to lists of source files
  my %dest_names = ();

  # check each directory for a HTML file
  foreach my $dir (@dirs) {
    my ($dh, $name, $file, $prog, $experiment);
    opendir($dh, $dir) or die("Unable to list files in directory: $!");
    while (($name = readdir($dh))) {
      $file = catfile($dir, $name);
      next if (-d $file);
      next unless ($name =~ m/^([a-zA-Z\-]+)\.html$/);
      # store the program name
      $prog = $1;
      # get the name of the last directory, which is 
      # assumed to describe the experiment
      $experiment = basename(dirname(abs_path($file)));
      last;
    }
    closedir($dh);
    # check that we found a file
    die("No MEME Suite HTML file found in directory: $dir") unless (defined($prog) && defined($experiment));
    # remove program name from end of the experiment description
    $experiment =~ s/\.$prog$//;
    # now store the destination name with a list of source files that would share the name
    my $dest_name = $prog . '.' . $experiment;
    if (defined($dest_names{$dest_name})) {
      push(@{$dest_names{$dest_name}}, $file);
    } else {
      $dest_names{$dest_name} = [$file];
    }
  }

  # copy files
  keys %dest_names; # reset hash iterator
  while (my ($dest_name, $source_files) = each %dest_names) {
    if (scalar(@{$source_files}) == 1) {
      # destination file is unique just from the experiment and program
      &cp($source_files->[0], catfile($dest, $dest_name . '.html'));
    } else {
      # destination file requires numbering to make unique
      for (my $i = 0; $i < scalar(@{$source_files}); $i++) {
        &cp($source_files->[$i], catfile($dest, $dest_name.'.'.($i+1).'.html'));
      }
    }
  }
}
&main();
1;