#!/bin/csh -f

#
# This shell script can run several commands,
# given two sequence files (DNA or protein) as input
#

# The -f option tells the script to ignore your .cshrc file

######## Check to make sure you get two arguments (sequence files)

if ($#argv != 2) then
	echo "Usage: $0 seq1 seq2"; exit 1
endif

# turn the arguments into better names
set seq1=$1
set seq2=$2

######## check to make sure each sequence file really exists

if (! -e $seq1) then
	echo $seq1 doesn't appear to exist; exit 1
endif
if (! -e $seq2) then
	echo $seq2 doesn't appear to exist; exit 1
endif

############  real commands start here  #############

# Do global alignment ("needle")

set globalOut=$seq1.$seq2.needle.out
needle $seq1 $seq2 -outfile $globalOut -filter
echo Global alignment: $globalOut

# Do local alignment ("water")

set localOut=$seq1.$seq2.water.out
water $seq1 $seq2 -outfile $localOut -filter
echo Local alignment: $localOut

echo All done!