#! /usr/bin/perl -w

##################################################################
# Predict beta pairing map for a singel sequence in fasta format
# Input: predict_ssa.sh, beta predictor, fasta file, output file
# Output foramt (name, seq, ss, bp1(all 0), bp2(all 0), matrix)

# Author: Jianlin Cheng, 3/15/2004
##################################################################

if (@ARGV != 4)
{
	die "need 4 parameters: ssa predictor, beta predictor, fasta input file, output file.\n"; 
}
$ssa_predictor = shift @ARGV;
$beta_predictor = shift @ARGV; 
$fasta_file = shift @ARGV;
$output_file = shift @ARGV; 

if (! -f $ssa_predictor)
{
	die "can't find the ss, sa predictor.\n"; 
}
if (! -f $beta_predictor)
{
	die "can't find beta predictor.\n"; 
}
if (! -f $fasta_file)
{
	die "can't find the fasta file.\n"; 
}
open(FASTA, "$fasta_file") || die "can't open fasta file.\n"; 
$target_name = <FASTA>; 
close FASTA;
$target_name = substr($target_name,1); 

#construct a temporay file for prediction of ss and sa
$pos = rindex($fasta_file, "/"); 
if ($pos < 0)
{
	$ssa_file = $fasta_file; 
}
else
{
	$ssa_file = substr($fasta_file, $pos+1); 
}
$ssa_file =~ s/\./_/g; 
$ssa_file .= "ssa"; 
$align_file = "${ssa_file}align"; 
`$ssa_predictor $fasta_file $ssa_file`; 
#notice: two files are generated from ssa predictor: one is ssa output, one is alignment file. 

#create tmp file for beta prediction
open(TMP, ">$output_file.bak") || die "can't create temporary file.\n"; 
open(INPUT, "$ssa_file") || die "can't open the ssa file.\n"; 
<INPUT>;
$seq = <INPUT>; 
chomp($seq); 
$ss = <INPUT>; 
chomp($ss); 
$sa = <INPUT>; 
chomp($sa); 
close INPUT; 
$length = length($seq); 
if ($length != length($ss) || $length != length($sa))
{
	die "sequence length doesn't match.\n"; 
}

print TMP "$target_name$seq\n$ss\n$sa\n";

#predict beta-mapping
system("$beta_predictor $output_file.bak $align_file $output_file"); 

#remove temporary files
`rm $output_file.bak`; 
`rm $ssa_file`; 
`rm $align_file`;