Permalink
Find file
Fetching contributors…
Cannot retrieve contributors at this time
executable file 96 lines (66 sloc) 2.43 KB
#!/bin/sh -
# this script will run SMART (http://smart.embl-heidelberg.de/) for an
# sequence input file or on each file in a file of filenames. it uses
# lynx to access send a query to the SMART web site and then writes
# the output to a file in the same way as run_fasta and run_blastp.
# see:
# http://www.sanger.ac.uk/Software/Artemis/stable/manual/runmenu.html#RUNMENU-CONFIGURATION
# for more details.
# you will need the "GET" command from the perl LWP module to use this script
# to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_smart,v 1.1 2004-06-09 10:03:12 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
if [ $# = 3 -a x$1 = x-onefile -o $# = 4 -a x$1 = x-onefile ]
then
shift
ONEFILE=t
else
if [ $# != 2 -a $# = != 1 ]
then
echo usage: $0 -onefile input_file output_file 1>&2
echo or: $0 file_of_filenames 1>&2
exit 1
fi
fi
# expand any ~ or environment variables
EXPANDED_PARAMETERS=`echo "echo $PARAMETERS" | /bin/csh -f`
### change this function to suit your site:
run_one_prog () {
INPUT_FILE=$1
OUTPUT_FILE=$2
PARAMETERS=$3
# remove the rubbish from the FASTA header and change the sequence
# into URL form
SEQUENCE=`perl -pne 'chomp; s/^>.*/>sequence/; s/ /\%20/g; $_ .= "%0D"' $INPUT_FILE`
SEQUENCE=`echo $SEQUENCE | sed 's/%0D$//'`
URL='http://smart.embl-heidelberg.de/smart/show_motifs.pl?INCLUDE_SIGNALP=INCLUDE_SIGNALP&DO_PROSPERO=DO_PROSPERO&DO_PFAM=DO_PFAM&SEQUENCE='"$SEQUENCE"
### change these lines:
EXEC=lynx
echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
echo "$OUTPUT_FILE" 1>&2
COMMAND="$EXEC -force_html -dump $URL"
echo "command line: $COMMAND" 1>&2
(echo "read from $URL"; echo) > $OUTPUT_FILE
$COMMAND 2>&1 >> $OUTPUT_FILE |
tee ${PROG}_errors.new 1>&2
#### end of changes
if [ -s ${PROG}_errors.new ]
then
( echo ERROR running $PROG: ; echo;
echo ===================================================
cat ${PROG}_errors.new ) >> $OUTPUT_FILE
cat ${PROG}_errors.new >> ${PROG}_errors
fi
}
(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
chmod a+x $PROG.kill
if [ x$ONEFILE = x ]
then
for i in `cat $1`
do
run_one_prog $i $i.out $EXPANDED_PARAMETERS
done
else
run_one_prog $1 $2 $EXPANDED_PARAMETERS
fi
exit 0