#! /bin/csh -f
#
# getMCHfof
#    Run all the files in a file of file names through "getMCH -SCF"
#
#    This program was written for Bill Rawlinson, and is intended for
#    his use only.
#
#    Usage: getMCHfof file_of_file_names
#

if ( $#argv != 1 ) then
	echo "Usage: getMCHfof file_of_file_names"
	exit 2
endif

if (! -e $1 ) then
	echo "No such file of file names"
	exit 2
endif

echo "Processing a file of file names through getMCH"
echo ""

# New fofn
set seq_fofn = ${1:r}.fofn
if (-e $seq_fofn) /bin/mv $seq_fofn ${seq_fofn}.$$
touch $seq_fofn

echo "Processing:"
foreach x ( `cat $1` )
	# This file of file name contains the sequence file names
	# Determine chromatogram file
	echo -n "   " $x
	set trace = ${x}.scf
	if (-e $x) /bin/mv $x ${x}.$$
	getMCH -SCF $trace -output $x -header 1
	if ($status != 0) then
		echo " - error in getMCH\!"
	else
		echo " - done"
		echo $x >> $seq_fofn
	endif
end

echo
echo "File of file names created:" $seq_fofn