#!/usr/bin/perl
#

#
# Wrapper for multicoil and ncoil to generate csv style output to STDOUT
# Pass it the complete path to the sequence or multicoil will complain
#
# multicoils ignored as it's a bitch to setup

use strict;
use warnings;
use POSIX;
use Jpred;

unless (@ARGV) { die("No arguments given\n"); }
goto NCOILS;
my ($path) = $ENV{'PWD'};
my ($file) = ($ARGV[0] =~ /.*\/(.*)/);
my ($multicoil) = ($ENV{'PAIRCOIL_CONFIG'} =~ /(.*)\/.*/);

# Print multicoils cmd file to temp file
my $multi_conf = tmpnam();
open(FILE, ">$multi_conf") or die($!);
print FILE "method = MultiCoil
bound = .5
no GUI
window length = 28
multi_lib 1 = 3 4 5
multi_lib 2 = 2 3 4
pair_lib = 1 2 4
conversion dir = $multicoil/CONVERSION_FILES/
table 1 = $multicoil/PROGRAM_DATA/cctb28
table 2 = $multicoil/PROGRAM_DATA/tritb28
pir = $multicoil/PROGRAM_DATA/sampled-pir.seq
genbnk = $multicoil/PROGRAM_DATA/genbnk
printfile dir = /homes/jon/jpred/src/MULTICOIL/TEST_RUNS/
log dir = $path/
seq scores dir = $path/ 
out dir = $path/";
close(FILE);

my $tmp2 = tmpnam();
xsystem("$BINDIR/readseq -f3 -p < $ARGV[0] > $tmp2");

# 1, 2, 3! We hate multicoil! Have to be in the same path as it's exe
# to run due to the hex editing on the multicoil exe to allow it to read
# some of its data files, also it requires PIR input file, sigh...
#my $pwd = $ENV{'PWD'};
#chdir("$JPREDROOT/src/MULTICOIL/");
#xsystem("$JPREDROOT/src/MULTICOIL/multicoil $tmp2 -config $multi_conf > /dev/null 2> /dev/null");
#chdir($pwd);

#my $co=0;
#my (@prob, @dimprob, @trimprob);

#$tmp2 =~ s/.*\///g;

#open(IN, "<$path/$tmp2.out") or die($!);
#while (<IN>) {
#	if (/^[#|%]/) { next; }
#	else {
#		@_ = split(" ", $_);
#		push @prob, $_[4];
#		push @dimprob, $_[5];
#		push @trimprob, $_[6];
#		}
#	}
#close(IN);

# remove junk
#unlink("$tmp2.out");
#unlink("$tmp2.seq_scores");
#unlink("$tmp2.log");
#unlink $multi_conf, $tmp2;

# Takes the prob. array and decides whether it's definitely a coil,
# maybe a coil, or not a coil.
sub coil {
	my @array;
	foreach (@_) {
		if ($_ >= 0.9) {
			push @array, "C";
			}
		elsif ($_ >= 0.5) {
			push @array, "c";
			}
		else {
			push @array, "-";
			}
		}
	return @array;
	}

# Prints a comma after each piece of data in array

sub print_cvs {
	foreach (@_) { print "$_,"; } 
}

#print "MULTCOIL:";
#print_cvs(coil(@prob));
#print "\n", "MULTCOIL_DIMER:";
#print_cvs(coil(@dimprob));
#print "\n", "MULTCOIL_TRIMER:";
#print_cvs(coil(@trimprob));
#print "\n";

#
# Finished with multicoil, now for lupas coils (?) Just runs ncoils with
# different -win values
#

sub ncoils {
	my ($file, $window) = @_;
	my @temp;
	open(PROG, "$BINDIR/ncoils -w -win $window < $file |") or die($!);
	open(REALDATA, ">$ARGV[0].lupas_$window") or die($!);
	while (<PROG>) {
		print REALDATA "$_";
		chop;
		push @temp, substr($_, 19, 5);
		}
	close(PROG);
	close(REALDATA);
	return @temp;
	}

NCOILS:
print "Lupas_21:";
print_cvs(coil(ncoils($ARGV[0], 21)));		# 21 window
print "\n", "Lupas_14:";
print_cvs(coil(ncoils($ARGV[0], 14)));		# 14 window
print "\n", "Lupas_28:";
print_cvs(coil(ncoils($ARGV[0], 28)));		# 28 window
print "\n";