#!/usr/bin/perl -w

if($#ARGV != 1)
{
   $prgName = `basename $0`;
   chop($prgName);
   die <<EOHELP;

Parses ambig noevio output file.

Usage: $prgName [monomer|dimer] 7col.noevio
EOHELP
}

$type = $ARGV[0];
$name = $ARGV[1];

$run = "grep -v '^#' $name";
$run .= " | /home/mnelson/bin/ambi/ambicrunch" if($type eq "dimer");
#don't do stringent of filtering here yet-- set buffer high so everything makes it through
$run .= " | /home/mnelson/bin/ambi/ambipick -b 5";
$run .= " | /home/mnelson/bin/ambi/ambimon -r 90" if($type eq "dimer");
$run .= " | /home/mnelson/bin/ambi/ambidis -c 8 -p 25.0";
$run .= " | /home/mnelson/bin/ambi/ambisingle";
$run .= " | /home/mnelson/bin/ambi/ambisplit -f $name.split" if($type eq "dimer");
#this type of filtering is done later
#$run .= " | /home/mnelson/bin/ambi/ambiring";
#$run .= " | /home/mnelson/bin/ambi/ambihnhx";
$run .= " | /home/mnelson/bin/ambi/ambichunk -l lib/peaklist";
$run .= " | /home/mnelson/bin/ambi/ambimark";
$run .= " | /home/mnelson/bin/ambi/ambisort -r 75";
$run .= " >> $name.filter";

system("echo \"# Date: `date`\" > $name.filter");
system("echo \"# $name parsed with:\" >> $name.filter");
system("echo \"# $run\" >> $name.filter");
system("grep \"^# ATOM A\" $name >> $name.filter");

system($run);