#!/usr/bin/env perl



# Perl wrapper script for rose.
#
#
#
# Jan Krueger <jkrueger@techfak.uni-bielefeld.de>


use File::Basename;

%rose_config;

foreach $m (split("##",join(' ',@ARGV))) {
    $m =~ s/^\s+//;
    $m =~ s/\s+$//;
    ($k,$v) = split(" *= *",$m);    
    $rose_config{$k} = $v if $k;
}


# add default parameter depending on InputType

if ($rose_config{InputType} == 4) { # DNA
    $rose_config{TheAlphabet} = "\"ACGT\"";
    
    if (!$rose_config{TheDNAmodel} || $rose_config{TheDNAmodel} eq "None") {
        delete $rose_config{TheDNAModel};
        $rose_config{ThePAMMatrix} = "[".
        "[.97,.01,.01,.01],".
        "[.01,.97,.01,.01],".
        "[.01,.01,.97,.01],".
        "[.01,.01,.01,.97]]";
    }
    $rose_config{TheFreq} = "[.25,.25,.25,.25]";

} elsif ($rose_config{InputType} == 20) { #AMINOACID
    $rose_config{TheAlphabet} = "\"ARNDCQEGHILKMFPSTWYV\"";
    $rose_config{ThePAMMatrix} = "[".
    "[9867.0,   2.0,   9.0,  10.0,   3.0,   8.0,  17.0,  21.0,   2.0,   6.0,   4.0,   2.0,   6.0,   2.0,  22.0,  35.0,  32.0,   0.0,   2.0,  18.0],".
"[   1.0,9913.0,   1.0,   0.0,   1.0,  10.0,   0.0,   0.0,  10.0,   3.0,   1.0,  19.0,   4.0,   1.0,   4.0,   6.0,   1.0,   8.0,   0.0,   1.0],".
"[   4.0,   1.0,9822.0,  36.0,   0.0,   4.0,   6.0,   6.0,  21.0,   3.0,   1.0,  13.0,   0.0,   1.0,   2.0,  20.0,   9.0,   1.0,   4.0,   1.0],".
"[   6.0,   0.0,  42.0,9859.0,   0.0,   6.0,  53.0,   6.0,   4.0,   1.0,   0.0,   3.0,   0.0,   0.0,   1.0,   5.0,   3.0,   0.0,   0.0,   1.0],".
"[   1.0,   1.0,   0.0,   0.0,9973.0,   0.0,   0.0,   0.0,   1.0,   1.0,   0.0,   0.0,   0.0,   0.0,   1.0,   5.0,   1.0,   0.0,   3.0,   2.0],".
"[   3.0,   9.0,   4.0,   5.0,   0.0,9876.0,  27.0,   1.0,  23.0,   1.0,   3.0,   6.0,   4.0,   0.0,   6.0,   2.0,   2.0,   0.0,   0.0,   1.0],".
"[  10.0,   0.0,   7.0,  56.0,   0.0,  35.0,9865.0,   4.0,   2.0,   3.0,   1.0,   4.0,   1.0,   0.0,   3.0,   4.0,   2.0,   0.0,   1.0,   2.0],".
"[  21.0,   1.0,  12.0,  11.0,   1.0,   3.0,   7.0,9935.0,   1.0,   0.0,   1.0,   2.0,   1.0,   1.0,   3.0,  21.0,   3.0,   0.0,   0.0,   5.0],".
"[   1.0,   8.0,  18.0,   3.0,   1.0,  20.0,   1.0,   0.0,9912.0,   0.0,   1.0,   1.0,   0.0,   2.0,   3.0,   1.0,   1.0,   1.0,   4.0,   1.0],".
"[   2.0,   2.0,   3.0,   1.0,   2.0,   1.0,   2.0,   0.0,   0.0,9872.0,   9.0,   2.0,  12.0,   7.0,   0.0,   1.0,   7.0,   0.0,   1.0,  33.0],".
"[   3.0,   1.0,   3.0,   0.0,   0.0,   6.0,   1.0,   1.0,   4.0,  22.0,9947.0,   2.0,  45.0,  13.0,   3.0,   1.0,   3.0,   4.0,   2.0,  15.0],".
"[   2.0,  37.0,  25.0,   6.0,   0.0,  12.0,   7.0,   2.0,   2.0,   4.0,   1.0,9926.0,  20.0,   0.0,   3.0,   8.0,  11.0,   0.0,   1.0,   1.0],".
"[   1.0,   1.0,   0.0,   0.0,   0.0,   2.0,   0.0,   0.0,   0.0,   5.0,   8.0,   4.0,9874.0,   1.0,   0.0,   1.0,   2.0,   0.0,   0.0,   4.0],".
"[   1.0,   1.0,   1.0,   0.0,   0.0,   0.0,   0.0,   1.0,   2.0,   8.0,   6.0,   0.0,   4.0,9946.0,   0.0,   2.0,   1.0,   3.0,  28.0,   0.0],".
"[  13.0,   5.0,   2.0,   1.0,   1.0,   8.0,   3.0,   2.0,   5.0,   1.0,   2.0,   2.0,   1.0,   1.0,9926.0,  12.0,   4.0,   0.0,   0.0,   2.0],".
"[  28.0,  11.0,  34.0,   7.0,  11.0,   4.0,   6.0,  16.0,   2.0,   2.0,   1.0,   7.0,   4.0,   3.0,  17.0,9840.0,  38.0,   5.0,   2.0,   2.0],".
"[  22.0,   2.0,  13.0,   4.0,   1.0,   3.0,   2.0,   2.0,   1.0,  11.0,   2.0,   8.0,   6.0,   1.0,   5.0,  32.0,9871.0,   0.0,   2.0,   9.0],".
"[   0.0,   2.0,   0.0,   0.0,   0.0,   0.0,   0.0,   0.0,   0.0,   0.0,   0.0,   0.0,   0.0,   1.0,   0.0,   1.0,   0.0,9976.0,   1.0,   0.0],".
"[   1.0,   0.0,   3.0,   0.0,   3.0,   0.0,   1.0,   0.0,   4.0,   1.0,   1.0,   0.0,   0.0,  21.0,   0.0,   1.0,   1.0,   2.0,9945.0,   1.0],".
"[  13.0,   2.0,   1.0,   1.0,   3.0,   2.0,   2.0,   3.0,   3.0,  57.0,  11.0,   1.0,  17.0,   1.0,   3.0,   2.0,  10.0,   0.0,   2.0,9901.0]".
"]";
    $rose_config{TheFreq} = "[.087,.041,.040,.047,.033,.038,.050,.089,.034,.037,.085,.081,.015,.040,.051,.070,.058,.010,.030,.065]";

} else {
    die "Unknown or Unset InputType parameter!";
}

# add general defaults
$rose_config{AlignmentFormat} = "\"FASTA\"";

#surround String Types with quotations
if ($rose_config{TheSequence}) {
    $rose_config{TheSequence} = "\"".$rose_config{TheSequence}."\"";
}
if ($rose_config{TheDNAmodel}) {
    $rose_config{TheDNAmodel} = "\"".$rose_config{TheDNAmodel}."\"";
}




# write config to current working dir
open (FH,"> rose.config") or die "$!";
for $k (keys(%rose_config)) {
    print FH "$k = $rose_config{$k} \n";
}
close(FH);


# call rose with generated config and split output into 3 files
open ($ROSESEQ, ">rose.fas") or die "$!";
open ($ROSETREE, ">rose.phy") or die "$!";

$basedir = dirname($0);
open (ROSE,"$basedir/rose.bin rose.config|") or die "$!";
while (<ROSE>) {
    chomp($_);
    if (/^Sequences:/) {
        $FH = $ROSESEQ;
    } elsif (/^Alignment:/) {
        $FH = STDOUT;
    } elsif (/^PHYLIP tree:/) {
        $FH = $ROSETREE;
    } else {
        print $FH $_,"\n" if $_;
    }
}
close(ROSE);
close($ROSESEQ);
close($ROSETREE);