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|
#! /bin/sh
#
# clean_jumbles file_name_root
#
comm=`echo $0 | sed 's&^.*/&&g'`
nosummaryflag="-nosummary"
summaryflag="-summary"
summary=1
while echo " $1" | grep "^ -" >/dev/null; do
if test $# -lt 2; then break
elif test $1 = "$nosummaryflag"; then summary=0; shift
elif test $1 = "-n"; then summary=0; shift
elif test $1 = "$summaryflag"; then summary=1; shift
elif test $1 = "-s"; then summary=1; shift
elif test $1 = "-"; then shift; break
else echo "Bad flag: $*"; shift $#; break
fi
done
if test $# -ne 1; then
echo "Usage: $comm [ $nosummaryflag ] file_name_root"
exit
fi
out="$1"
# Check requested name
if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -eq 0; then
echo "$comm: No files found of form $out.(jumble_seed)"
exit
elif grep '^Ln Likelihood' $out.[0-9]* >/dev/null; then :
else
echo "$comm: No likelihoods found in files of form $out.(jumble_seed)"
exit
fi
# Summary exists
summarized=0
if test -f "$out.summary" -a $summary -gt 0; then
if test ! -f "$out.tree" -o ! -f "$out.out"; then
echo "
$comm: Summary file $out.summary exists, but corresponding output
and tree files ($out.out and $out.tree) cannot be found.
Cleaning aborted.
"
exit
else
echo "
Summary file $out.summary exists. New jumbles will be added to that
summary without further checking.
"
summarized=1
fi
fi
# Don't clobber an existing file
if test $summarized -eq 0 -a \( -f "$out.tree" -o -f "$out.out" \); then
echo "
$comm: File(s) with the name(s) $out.out and/or $out.tree
already exist and would be clobbered by 'cleaning' the jumble output files.
Move them to a new name and try again.
"
exit
fi
# Find best file PID with the given name
if test $summarized -eq 0; then
pid=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
sed 's/^\(.*\):Ln Like.*=\(.*\)$/\2 \1/' |
sort -nr +0 | head -1 | sed -e 's/^[^ ]* //' -e 's/^.*\.//'`
fi
# Write score summary file, if requested
if test $summary -gt 0; then
if test $summarized -eq 0; then
grep '^Ln Likelihood' $out.[0-9]* /dev/null |
sed 's/^\(.*\):\(Ln Like.*\)$/\2 (file: \1)/' |
sort -nr +3 > "$out.summary"
else
temp_name="$out.`uname -n`.$$"
mv "$out.summary" "$temp_name"
grep '^Ln Likelihood' $out.[0-9]* /dev/null |
sed 's/^\(.*\):\(Ln Like.*\)$/\2 (file: \1)/' |
cat "$temp_name" - |
sort -nr +3 > "$out.summary"
rm -f "$temp_name"
fi
fi
# Move output and treefile to new names
if test $summarized -eq 0; then
oldname="$out.$pid"
if grep "^Ln Likelihood" "$oldname" >/dev/null; then
newname="$out.out"
treenew="$out.tree"
treeold="treefile.$pid"
checkpt="checkpoint.$pid"
if test -f "$treeold"; then mv "$treeold" "$treenew"
elif test -f "$checkpt"; then tail -1 "$checkpt" >"$treenew"
else echo "$comm: Cannot find tree file. Cleaning aborted."; exit
fi
mv "$oldname" "$newname"
rm -f "$checkpt"
fi
fi
# Remove other output, tree and checkpoint files:
if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -gt 0; then
pids=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
sed -e 's/^\(.*\):Ln Like.*$/\1/' -e 's/^.*\.//'`
for pid in $pids; do
rm -f "$out.$pid" "treefile.$pid" "checkpoint.$pid"
done
fi
|
