the bash alternative for run_TA

run_TA (text/plain), 1.10 KB, created by dawe on 2007-04-27 13:53:00 UTC

#!/bin/sh

# Copyright @ 2000 The Institute for Genomic Research (TIGR). All rights
# reserved.
#
# This software is provided "AS IS". The Institute for Genomic Research makes
# no warranties, express or implied, including no representation or warranty
# with respect to the performance of the software and derivatives or their
# safety, effectiveness, or commercial viability. TIGR does not warrant the
# merchantability or fitness of the software and derivatives for any
# particular purpose, or that they may be exploited without infringing the
# copyrights, patent rights or property rights of others.
#
# This software program may not be sold, leased, transferred, exported or
# otherwise disclosed to anyone, in whole or in part, without written consent
# of TIGR.

if [ ! -e "$1" ] 
then
	asmg_options=$1
	shift
else
	asmg_options=""
fi

for file in $*
do
	file_tail=`basename  $file`
	file_root=${file_tail%%.*}
	/usr/bin/TIGR_Assembler -n ${file_root} -g 8 -l 40 -e 15 -p 97.5 -a ${file_root}.align -f ${file_root}.fasta ${asmg_options} ${file_root}.scratch < ${file} > ${file_root}.asm 2> ${file_root}.error
done