#!/usr/bin/perl -w
# Badri Adhikari, 9-9-2017

use strict;
use warnings;
use Carp;
use Cwd 'abs_path';
use File::Basename;

####################################################################################################
my $fasta_dir = shift;
my $aln_dir = shift;
my $ccmpred_dir = shift;
my $pdb_dir = shift;
my $tool_dir = shift;

my $evaluate_script = abs_path(dirname($0))."/convert_ccmpred_rr.pl";
#system("rm -rf ${ccmpred_dir}/*");
my @pdbs = ();
my @files = glob("${pdb_dir}/*.pdb");
foreach my $file (@files){
    my $id = basename($file);
    $id =~ s{\.[^.]+$}{};
    push(@pdbs, $id)
}

@files = glob("${aln_dir}/*.aln");
foreach my $file (@files){
    my $id = basename($file);
    $id =~ s{\.[^.]+$}{};
    foreach my $pdb (@pdbs){
        if($pdb =~ m/^$id/){
                system_cmd("${evaluate_script} ${fasta_dir}/$id.fasta $file ${ccmpred_dir}/$id.ccmpred ${pdb_dir}/$pdb.pdb ${tool_dir}");
                print($pdb." ");
                my $exit_code = system("grep \"$id.ccmpred.rr (precision)\" ${ccmpred_dir}/precision.txt");
                if($exit_code){
                     print("no long-range contacts\n");
                }
				system("grep \"$id.ccmpred.rr (precision)\" ${ccmpred_dir}/precision.txt >> ${ccmpred_dir}/results.txt");
        }
    }
}

####################################################################################################
sub system_cmd{
    my $command = shift;
    my $log = shift;
    confess "EXECUTE [$command]?\n" if (length($command) < 5  and $command =~ m/^rm/);
    if(defined $log){
        system("$command &> $log");
    }
    else{
        #print "[[Executing: $command]]\n";
        system($command);
    }
    if($? != 0){
        my $exit_code  = $? >> 8;
        confess "ERROR!! Could not execute [$command]! \nError message: [$!]";
    }
}

####################################################################################################
sub count_lines{
    my $file = shift;
    my $lines = 0;
    return 0 if not -f $file;
    open FILE, $file or confess "ERROR! Could not open $file! $!";
    while (<FILE>){
        chomp $_;
        $_ =~ tr/\r//d; # chomp does not remove \r
        next if not defined $_;
        next if length($_) < 1;
        $lines ++;
    }
    close FILE;
    return $lines;
}

####################################################################################################
sub seq_fasta{
    my $file_fasta = shift;
    confess "ERROR! Fasta file $file_fasta does not exist!" if not -f $file_fasta;
    my $seq = "";
    open FASTA, $file_fasta or confess $!;
    while (<FASTA>){
        next if (substr($_,0,1) eq ">");
        chomp $_;
        $_ =~ tr/\r//d; # chomp does not remove \r
        $seq .= $_;
    }
    close FASTA;
    return $seq;
}

####################################################################################################
sub ccmpred2rr{
    my $file_fasta = shift;
    my $file_ccmpred = shift;
    my $file_rr = shift;
    my $seq_sep_th = shift;
    confess "ERROR! file_fasta not defined!" if !$file_fasta;
    confess "ERROR! file_ccmpred not defined!" if !$file_ccmpred;
    confess "ERROR! file_rr not defined!" if !$file_rr;
    confess "ERROR! seq_sep_th not defined!" if !$seq_sep_th;
    my %conf = ();
    open CCM, $file_ccmpred or confess $!;
    my $i = 1;
    while(<CCM>){
        my @C = split /\s+/, $_;
        for(my $j = 0; $j <= $#C; $j++){
            my $pair = $i." ".($j+1);
            $pair = ($j+1)." ".$i if ($j+1) < $i;
            my $confidence = $C[$j];
            $confidence = $conf{$pair} if (defined $conf{$pair} && $conf{$pair} > $confidence);
            $conf{$pair} =  sprintf("%.3f",$confidence);
        }
        $i++;
    }
    close CCM;
    open RR, ">$file_rr" or confess $!;
    print RR "".seq_fasta($file_fasta)."\n";
    foreach (sort {$conf{$b} <=> $conf{$a}} keys %conf){
        my @C = split /\s+/, $_;
        next if abs($C[0] - $C[1]) < $seq_sep_th;
        print RR $_." 0 8 ".$conf{$_}."\n";
    }
    close RR;
}

####################################################################################################
sub seq_rr{
    my $file_rr = shift;
    confess ":(" if not -f $file_rr;
    my $seq;
    open RR, $file_rr or confess "ERROR! Could not open $file_rr! $!";
    while(<RR>){
        chomp $_;
        $_ =~ tr/\r//d; # chomp does not remove \r
        $_ =~ s/^\s+//;
        next if ($_ =~ /^>/);
        next if ($_ =~ /^PFRMAT/);
        next if ($_ =~ /^TARGET/);
        next if ($_ =~ /^AUTHOR/);
        next if ($_ =~ /^SCORE/);
        next if ($_ =~ /^REMARK/);
        next if ($_ =~ /^METHOD/);
        next if ($_ =~ /^MODEL/);
        next if ($_ =~ /^PARENT/);
        last if ($_ =~ /^TER/);
        last if ($_ =~ /^END/);
        # Now, I can directly merge to RR files with sequences on top
        last if ($_ =~ /^[0-9]/);
        $seq .= $_;
    }
    close RR;
    $seq =~ s/\s+//;
    confess ":( no sequence header in $file_rr" if not defined $seq;
    return $seq;
}

####################################################################################################
sub wrap_seq{
    my $seq = shift;
    confess ":(" if !$seq;
    my $seq_new = "";
    while($seq){
        if(length($seq) <= 50){
            $seq_new .= $seq;
            last;
        }
        $seq_new .= substr($seq, 0, 50)."\n";
        $seq = substr($seq, 50);
    }
    return $seq_new;
}