#!/usr/local/bin/perl -w
#
#
#
#        Function: Creates predict-2nd training file specification input
#                  from a list of chain ids. 
#		Just creates the file reads for target98 and 2d sequences
#		Note: this script updates and replaces "script-input-from-ids".
#
#        Usage: reads-from-ids -a2m t99 -2d mixed.2d < foo.ids > foo.script
#
#	Options:
#		-a2m	t2k-thin90	default alignment
#			(other alignments as specified in $SUBDIR below)
#
#		-2d	stride-mixed.2d	default right answer
#
# 		-repeat_2d 1		number of times to repeat 
#			the "right answer" file (for neural nets with multiple trainable layers)
#
#
#######################################################################

# NEEDS TO BE REWRITTEN TO USE THE ChainIds.pm module!


use English;
use File::Basename;
use lib "/projects/compbio/experiments/models.97/scripts";
use ChainIds;

    

# Main routine
{
    &process_command_line;

    $a2m_suffix = ChainIds::get_suffix($alignspec);
    $struct_suffix = ChainIds::get_suffix($structspec);

    ChainIds::ReadIDsFH(STDIN, %ids);
    
    print "InfilePrefix\n";
    foreach $id (keys %ids)
    {

	my $a2mfile = ChainIds::full_existing_filename($id,$alignspec,@models97_subdir_list);

	if (! defined($a2mfile))
	{   print STDERR "Error: can't find $id for $a2m_suffix\n";
	    next;
	}

	my $structfile = ChainIds::full_existing_filename($id,$structspec,@models97_subdir_list);
	if (! defined($structfile))
	{   print STDERR "Error: can't find $id for $struct_suffix\n";
	    next;
	}
	
	print "ReadTrain $a2mfile";
	for(1..$repeat_2d)
	{   print " $structfile"
	}
	print "\n\n";
    }

}

#------------------------ subroutines --------------------------------


sub process_command_line 
{
    local($i) = 0;

    # Check for even number of command line words
    if ($#ARGV%2 != 1) 
    {   print "ERROR: Command line error.\n";
        exit (-1);
    }

    # Set default values
    $alignspec = "t2k-thin90";
    $structspec = "stride-mixed.2d";
    $repeat_2d = 1;

    # Get user specified values
    while ($i <= $#ARGV) 
    {
        $_ = $ARGV[$i++];
        if (/^-a2m/)
	{	$alignspec     =    $ARGV[$i++]; 
	}
	elsif (/^-2d/)
	{	$structspec     =    $ARGV[$i++]; 
	}	    
	elsif (/^-repeat_2d/)
	{	$repeat_2d     =    $ARGV[$i++]; 
	}	    
	else
	{    print STDERR "ERROR: unrecognized argment $_\n";
	    exit(1);
        }
    }

    # Make certain that there are now values for those parameters with non-
    # default values
    if ($#models97_subdir_list<0) 
    {    @models97_subdir_list = ("pdb");
    }
    
    return;
}

# prepend relative path names with current working directory
# usage $absolute_file = absolute($file)

sub absolute($)
{
        my ($file) = @_;
        return $file if ($file =~ /^\/.*/);
        my $wd = `pwd`;
        chomp($wd);
        if ($wd=~/\/auto(.*)/) {return "$1/$file"};
        return "$wd/$file";

}