#!/opt/conda/conda-bld/viennarna_1717709120079/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/perl -w
# -*-Perl-*-
# Last changed Time-stamp: <2008-08-26 16:04:00 ivo>
# produce Pauline Hogeweg's mountain representation *_dp.ps files
# writes 3 sets of x y data separated by a "&"
# the first two sets are mountain representations from base pair probabilities
# and mfe structure, respectively.
# definition: mm[i],mp[i] = (mean) number of base pairs enclosing base i
# third set a measure of well-definedness: the entropy of the pair probs of
# base i, sp[i] = -Sum p_i * ln(p_i). Well-defined regions have low entropy.
#
# use e.g. as  mountain.pl dot.ps | xmgrace -pipe

use strict;
our (@mm, @mp, @pp, @sp, @p0, $i, $max, $length, $do_png);  # perl5 only

my $sep = "&";   # xmgr uses & to separate data sets

if (@ARGV && ($ARGV[0] eq '-png')) {
    eval "use Chart::Lines";
    die($@,
        "\nCould not load the Chart::Lines module required with -png option\n")
        if $@;
    $do_png=1;
    shift;
}


while (<>) {
    chomp;
    if (/\/sequence \{ \((\S*)[\\\)]/) {
        my $seq = $1;           # empty for new version
        while (!/\) \} def/) {  # read until end of definition
            $_ = <>;
            /(\S*)[\\\)]/;      # ends either with `)' or `\'
            $seq .= $1;
        }
        $length = length($seq);
        next;
    }

    next unless /(\d+) (\d+) (\d+\.\d+) (.box)$/;
    my ($i, $j, $p, $id) = ($1,$2,$3,$4);
    if ($id eq "ubox") {
        $p *= $p;           # square it to probability
        $mp[$i+1] += $p;
        $mp[$j]   -= $p;
        my $ss = $p>0 ? $p*log($p) : 0;
        $sp[$i] += $ss;
        $sp[$j] += $ss;
        $pp[$i] += $p;
        $pp[$j] += $p;
    }
    if ($id eq "lbox") {
        $mm[$i+1]++;
        $mm[$j]--;
    }
}
$mp[0] = $mm[0] = $max = 0;
for ($i=1; $i<=$length; $i++) {
    no warnings;
    $mp[$i]+=$mp[$i-1];
    $max = $mp[$i] if ($mp[$i]>$max);
    $mm[$i]+=$mm[$i-1];
    $max = $mp[$i] if ($mp[$i]>$max);
    $sp[$i] += (1-$pp[$i])*log(1-$pp[$i]);
}

if ($do_png) {
    my $width =  800;
    my $height = 600;

    # FIXME: legend_lables when doing mfe only
    my $skip = 10**(int (log($length)/log(10.) - 0.5));
    my $obj = Chart::Lines->new( $width, $height );
    $obj->set ('title' => $ARGV,
               'x_label' => 'Position',
               'y_label' => 'Height',
               'min_val' => 0,
               'precision' => 0,
               'legend_labels' => ['mfe', 'pf'],
               'skip_x_ticks' => $skip);

    $obj->add_dataset ((0..$length));

    $obj->add_dataset (@mp);
    $obj->add_dataset (@mm);
    $obj->png("mountain.png");

} else {
    # print the results for plotting
    for ($i=1; $i<=$length; $i++) {
        printf("%4d  %7.5g\n", $i, $mp[$i]);
    }
    print "$sep\n";

    for ($i=1; $i<=$length; $i++) {
        printf("%4d  %4d\n", $i, $mm[$i]);
    }
    print "&\n";
    my $log2 = log(2);
    for ($i=1; $i<=$length; $i++) {
        printf("%4d  %7.5g\n", $i, -$sp[$i]/$log2);
    }
}

=head1 NAME

mountain - produce coordinates for a mountain plot from a dot plot

=head1 SYNOPSIS

  mountain.pl myseq_dp.ps > mountain.dat

=head1 DESCRIPTION

reads pair probabilities and MFE structure from a probability dot
plot as produced by C<RNAfold -p>, and produces x-y data suitable
for producing a mountain plot using standard xy-plotting programs.

Output consists of 3 data sets separated by a line containing only
the C<&> character. The first two sets are mountain representations
computed from base pair probabilities and mfe structure, respectively.
For the mfe case the moutain plot graphs the number base pairs
enclosing a position k, in case of pair probabilities we use the average
number of base pairs computed as m_k = \Sum_i<k<j p_ij.
The third set contains the positional entropy, which provides a measure
of local structural welldefinedness, s_i = -\Sum_j p_ij * ln(p_ij).

=head1 EXAMPLE

The output is suitable for graphing with xmgrace, e.g.:
C<RNAfold -p < foo.seq; mountain.pl foo_dp.ps | xmgrace -pipe>

=head1 AUTHOR

Ivo L. Hofacker <ivo@tbi.univie.ac.at>

=cut
