#!/bin/env perl

=pod

=head1 NAME

clustalparser - SOME KIND OF DESCRIPTION

=head1 SYNOPSIS

  # parse alignments
  cat FILE | ./clustalparser
  ./clustalparser -in FILE
 
  # get help or see man page
  ./clustalparser [-help] [-man]

=head1 DESCRIPTION

You should describe what this does.

=head1 OPTIONS

=head2 -in FILE

Specify input file. You can also pipe the file via STDIN

  cat FILE | ./clustalparser

=head2 -help

Get brief help

=head2 -man

Show man page.

=cut

use strict;
use diagnostics;
use warnings FATAL=>"all";

use Carp;
use Config::General;
use Cwd qw(getcwd abs_path);
use Data::Dumper;
use File::Basename;
use FindBin;
use Getopt::Long;
use List::MoreUtils qw(uniq minmax);
use Math::Round qw(round nearest);
use Math::VecStat qw(sum min max average);
use Pod::Usage;
use Statistics::Basic qw(median stddev);
use Storable;
use lib "$FindBin::RealBin";
use lib "$FindBin::RealBin/../lib";
use lib "$FindBin::RealBin/lib";

our (%OPT,%CONF,$conf);
our @COMMAND_LINE = (
                     "in=s",
										 "configfile=s",
										 "help",
										 "cdump",
										 "man",
										 "debug");

# read and parse configuration file
parse_config();

sub validateconfiguration {
}

# _START

# This is a boilerplate Perl script for you to edit to build up a clustal parser
#
# Run it first as
#
# ./clustalpaser -h
#
# and then using the alignment file
#
# cat ../../data/alignment.aln | ./clustalparser

my $data = read_file($CONF{in});

# dump the data structure we created from the
# alignments to STDOUT

printdumper($data);

# Continue with the script here

# ...

################################################################

# Convert a list of numbers into a
# list of contiguous ranges defined by [min,max] 
#
# [ [min1,max1], [min2,max2], ...]
sub list2ranges {
  my @x = sort {$a <=> $b} @_;
  my $ranges = [];
  # I wrote two approaches to solve this problem. The first
  # is more like C code and the second is more Perlish.
  # Change the 1 to a 0 in the outer if loop to use the second approach.
  # Which one reads easier?
  if(1) {
    # This one is more like C
    for ( my $i = 0; $i < @x; $i++) {
      my $min = $i;
      for my $j ($i+1..@x-1) {
        if($x[$j] - $x[$j-1] > 1) {
          last;
        }
        $i = $j;
      }
      push @$ranges, [$min,$i];
    }
  } else {
    # This one is more Perlish
    my $i = 0;
    my $max;
    while(@x) {
      my $x = shift @x;
      if(! defined $ranges->[-1] || $x - $max > 1) {
        push @$ranges, [$i,$i];
      } else {
        $ranges->[-1][1] = $i;
      }
      $max = $x;
      $i++;
    }
  }
  return $ranges;
}

# Read the alignment file. For now, all it does
# is read the alignment lines and store them
# as a hash, keyed by the sequence id.
sub read_file {
	my $file        = shift;
	my $inputhandle = get_handle($file);
	my $data;
	while(<$inputhandle>) {
    # skip the first line, which is a header
    # this is one of those rare times that a special variable
    # other than $_ or @_ is usedful. The $. gives the
    # line number of the file handle that is currently being read.
    next if $. == 1;
    # skip comments and blank lines
		next if /^\s*\#/ ||/^\s*$/;
    # trim newline
		chomp;
    # you now have the fields of this line
		my ($id,$seq,$cumul) = split;
    # put these values into a hash and push it onto the list
		push @$data, {id=>$id,
                  seq=>$seq,
                  cumul=>$cumul};
                  
	}
	return $data;
}

# _END

sub get_handle {
	my $file = shift;
	my $h;
	if($file) {
		die "No such file [$file]" unless -e $file;
		open(FILE,$file);
		$h = \*FILE;
	} else {
		$h = \*STDIN;
	}
	return $h;
}

# HOUSEKEEPING ###############################################################

sub dump_config {
	printdumper(\%OPT,\%CONF);
}

sub parse_config {
  my $dump_debug_level = 3;
  GetOptions(\%OPT,@COMMAND_LINE);
  pod2usage() if $OPT{help};
  pod2usage(-verbose=>2) if $OPT{man};
  loadconfiguration($OPT{configfile});
  populateconfiguration();	# copy command line options to config hash
  validateconfiguration(); 
  if ($CONF{cdump}) {
    $Data::Dumper::Indent    = 2;
    $Data::Dumper::Quotekeys = 0;
    $Data::Dumper::Terse     = 0;
    $Data::Dumper::Sortkeys  = 1;
    $Data::Dumper::Varname = "OPT";
    printdumper(\%OPT);
    $Data::Dumper::Varname = "CONF";
    printdumper(\%CONF);
    exit;
  }
}

sub populateconfiguration {
  for my $var (keys %OPT) {
    $CONF{$var} = $OPT{$var};
  }
  repopulateconfiguration(\%CONF);
}

sub repopulateconfiguration {
  my ($node,$parent_node_name) = shift;
  return unless ref($node) eq "HASH";
  for my $key (keys %$node) {
		my $value = $node->{$key};
		if (ref($value) eq "HASH") {
			repopulateconfiguration($value,$key);
		} elsif (ref($value) eq "ARRAY") {
			for my $item (@$value) {
				repopulateconfiguration($item,$key);
			}
		} elsif (defined $value) {
			my $new_value = parse_field($value,$key,$parent_node_name,$node);
			$node->{$key} = $new_value;
		}
	}
}

sub parse_field {
	my ($str,$key,$parent_node_name,$node) = @_;
	# replace configuration field
	# conf(LEAF,LEAF,...)
	while ( $str =~ /(conf\(\s*(.+?)\s*\))/g ) {
		my ($template,$leaf) = ($1,$2);
		if (defined $template && defined $leaf) {
			my @leaf         = split(/\s*,\s*/,$leaf);
			my $new_template;
			if (@leaf == 2 && $leaf[0] eq ".") {
				$new_template = $node->{$leaf[1]};
			} else {
				$new_template = fetch_conf(@leaf);
			}
			$str =~ s/\Q$template\E/$new_template/g;
		}
	}
	if ($str =~ /\s*eval\s*\(\s*(.+)\s*\)/) {
		my $fn = $1;
		$str = eval $fn;
		if ($@) {
			die "could not parse configuration parameter [$@]";
		}
	}
	return $str;
}

sub fetch_configuration {
	my @config_path = @_;
	my $node        = \%CONF;
	if(! @config_path) {
		return \%CONF;
	}
	for my $path_element (@config_path) {
		if (! exists $node->{$path_element}) {
	    return undef;
		} else {
	    $node = $node->{$path_element};
		}
	}
	return $node;
}

sub fetch_conf {
	return fetch_configuration(@_);
}

################################################################
#
#

sub loadconfiguration {
  my $file = shift;
  if (defined $file) {
    if (-e $file && -r _) {
      # provided configuration file exists and can be read
      $file = abs_path($file);
    } else {
      confess "The configuration file [$file] passed with -configfile does not exist or cannot be read.";
    }
  } else {
    # otherwise, try to automatically find a configuration file
    my ($scriptname,$path,$suffix) = fileparse($0);
    my $cwd     = getcwd();
    my $bindir  = $FindBin::RealBin;
    my $userdir = $ENV{HOME};
    my @candidate_files = (
													 "$cwd/$scriptname.conf",
													 "$cwd/etc/$scriptname.conf",
													 "$cwd/../etc/$scriptname.conf",
													 "$bindir/$scriptname.conf",
													 "$bindir/etc/$scriptname.conf",
													 "$bindir/../etc/$scriptname.conf",
													 "$userdir/.$scriptname.conf",
													);
    my @additional_files = ();
    for my $candidate_file (@additional_files,@candidate_files) {
			#printinfo("configsearch",$candidate_file);
			if (-e $candidate_file && -r _) {
				$file = $candidate_file;
				#printinfo("configfound",$candidate_file);
				last;
			}
    }
  }
  if (defined $file) {
    $OPT{configfile} = $file;
    $conf = new Config::General(
																-ConfigFile=>$file,
																-IncludeRelative=>1,
																-IncludeAgain=>1,
																-ExtendedAccess=>1,
																-AllowMultiOptions=>"yes",
																-LowerCaseNames=>1,
																-AutoTrue=>1
															 );
    %CONF = $conf->getall;
  }
}

sub printdebug {
	printerr(@_) if defined $CONF{debug};
}

sub printinfo {
	print join(" ",map { defined $_ ? $_ : "_undef_" } @_),"\n";
}

sub printfinfo {
	my ($fmt,@args) = @_;
	@args = map { defined $_ ? $_ : "_undef_" } @args;
	printf("$fmt\n",@args);
}

sub printerr {
	print STDERR join(" ",map { defined $_ ? $_ : "_undef_" } @_),"\n";
}

sub printdumper {
	print Dumper(@_);
}

sub printdumperq {
  printdumper(@_);
  exit;
}

=pod 

=head1 HISTORY

=over

=item * 17 Oct 2018

Boilerplate created.

=back 

=head1 AUTHOR

Martin Krzywinski

=head1 CONTACT

Martin Krzywinski
Genome Sciences Center
BC Cancer Research Center
100-570 W 7th Ave
Vancouver BC V5Z 4S6

mkweb.bcgsc.ca
martink@bcgsc.ca

=cut