#!/usr/local/bin/perl
#
# This script is a simplified interface to the commands in the makefile.
# What the goal is here is to get the alignment that would be produced
# if rather than aligning the template and target sequences to the model,
# the entire seed alignment was aligned to the model along with the target
# sequence.  This gives us the input alignment necessary for 
# build-trimming-info.
# 
# Commands (in order of position)
#	targetSeq:		name of a file containing the target sequence
#	modelName:		name of the model that we will align to
#	trainingSeqs:	file containing the alignment used to train the model
#	runName:		forms the name for the output alignment
#	cmdOptions:		alignment command options which vary between alignments
#					
#
	use strict;
	my ($targetSeq, $modelName, $trainingSeqs, $runName, $cmd, @cmdOptions, 
	    $ii);

	$targetSeq = shift;
	$modelName = shift;
	$trainingSeqs = shift;
	$runName = shift;
	@cmdOptions = @ARGV;

    $cmd = "hmmscore $runName -i $modelName -db $targetSeq -db $trainingSeqs";
	$cmd .= " -subtract_null 4 -simplethreshold 1 -select_align 8";
    for $ii (0 .. $#cmdOptions) {
	    $cmd .= " " . $cmdOptions[$ii];
	}	
    print "cmd is $cmd\n";
	system($cmd);