#!/bin/csh
#
#This software is Copyright (C) 2005 by Andrew Firth, University of Otago, 
#Dunedin, New Zealand. All rights reserved.
#
#Script to redo the mlrgd part of run_mlrgd script for different parameters.
limit stacksize unlimited
setenv PATH ${PATH}:${HOME}/bin

@ argc = `echo $argv | awk '{print NF}'`
if ($argc != 17) then
  echo "Usage: redo_mlrgd prefix tttmin tttmax tVfit maxiter fitwhat refpos"\
       "circular wholeseq range1 range2 Vfix Vtype Vmin Vmax skip newprefix"
  exit
endif

set prefix = $1
set tttmin = $2
set tttmax = $3
set tVfit = $4
set maxiter = $5
set fitwhat = $6
set refpos = $7
set circular = $8
set wholeseq = $9
set range1 = $10
set range2 = $11
set Vfix = $12
set Vtype = $13
set Vmin = $14
set Vmax = $15
set skip = $16
set newprefix = $17

cp TIDYUP/seq.???.aln .
cp TIDYUP/orfs.??? .
cp TIDYUP/*.dat .

echo -n "Running MLRGD..."

echo $prefix.pairs "   " > setup.mlrgd
echo $tttmin $tttmax $tVfit $maxiter "   #t fitting params" >> setup.mlrgd
echo $fitwhat "   #fitwhat" >> setup.mlrgd
echo 0 "   #model" >> setup.mlrgd                 #non-coding model
echo $refpos "   #refpos" >> setup.mlrgd
echo $circular "   #circular" >> setup.mlrgd
echo $wholeseq $range1 $range2 "   #nt range params" >> setup.mlrgd
echo $Vfix $Vtype $Vmin $Vmax "   #V fitting params" >> setup.mlrgd
echo $skip "   #ambiguous nt" >> setup.mlrgd
mlrgd setup.mlrgd >> $prefix.errorlog || exit
mv mlrgd_out.dat    $newprefix.nc.dat
mv mlrgd_out.log    $newprefix.nc.log
mv mlrgd_out.plot   $newprefix.nc.plot
mv mlrgd_out.info   $newprefix.nc.info

echo $prefix.pairs "   " > setup.mlrgd
echo $tttmin $tttmax $tVfit $maxiter "   #t fitting params" >> setup.mlrgd
echo $fitwhat "   #fitwhat" >> setup.mlrgd
echo 1 "   #model" >> setup.mlrgd                 #full-coding model
echo $refpos "   #refpos" >> setup.mlrgd
echo $circular "   #circular" >> setup.mlrgd
echo $wholeseq $range1 $range2 "   #nt range params" >> setup.mlrgd
echo $Vfix $Vtype $Vmin $Vmax "   #V fitting params" >> setup.mlrgd
echo $skip "   #ambiguous nt" >> setup.mlrgd
mlrgd setup.mlrgd >> $prefix.errorlog || exit
mv mlrgd_out.dat    $newprefix.fc.dat
mv mlrgd_out.log    $newprefix.fc.log
mv mlrgd_out.plot   $newprefix.fc.plot
mv mlrgd_out.info   $newprefix.fc.info

rm -f seq.???.aln orfs.??? seqs.dat aa2codon.dat aa.dat codon.dat nuc.dat

echo "Done"