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#!/bin/sh -
# this script will run clustalx on a temporary file containing the concatenated
# contents of files listed in a file of filenames
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_clustalx,v 1.3 2005-02-21 11:50:01 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
if [ $# != 1 ]
then
echo usage: $0 file_of_filenames
fi
(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
chmod a+x $PROG.kill
file_of_filenames=$1
date=`date +"%y_%m_%d"`
hostname=`hostname`
temp_file_name=/tmp/artemis_temp.$$.$hostname.$date.clustalx_input.fasta
cat $file_of_filenames | xargs cat > $temp_file_name
# make sure that the identifiers are unique for clustalx
perl -pne 'if (/^>(\S+)/) {
$name = $1;
if (exists $h{$name}) {
$i = $h{$name}++;
s/^>(\S+)/>$name.$i/;
} else {
$h{$name} = 0;
}
}' $temp_file_name > $temp_file_name.processed
clustalx -INFILE=$temp_file_name.processed
exit 0
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