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|
#! /bin/sh
#
comm=`echo "$0" | sed -e 's&^.*/&&'`
cleanflag="-noclean"
maxflag="-max"
niceflag="-nice"
stdopt=""
jumbles=10
nice=10
cleanUp=1
# The spaces in the echo and grep are required because of a "feature" that
# causes /bin/sh echo to consume ANY leading argument that begins with -n.
while echo " $1" | grep "^ -" >/dev/null; do
if test $# -lt 2; then break
elif test $1 = $maxflag; then jumbles=$2; shift; shift
elif test $1 = "-m"; then jumbles=$2; shift; shift
elif test $1 = $cleanflag; then cleanUp=0; shift
elif test $1 = "-c"; then cleanUp=0; shift
elif test $1 = $niceflag; then nice=$2; shift; shift
elif test $1 = "-n"; then nice=$2; shift; shift
elif test $1 = "-"; then shift; break
else echo "Bad flag: $*"; while test $# -gt 0; do shift; done; break
fi
done
if test $# -eq 2; then
opts="$stdopt"
elif test $# -eq 3; then
if test -n "$3"; then opts="$stdopt | $3"
else opts="$stdopt"
fi
else
cleanprm="[$cleanflag]"
maxprm="[$maxflag maxjumble]"
niceprm="[$niceflag nicevalue]"
optprm="[ "'"'"dnaml_opt1 [ | dnaml_opt2 [...]]"'"'" ]"
echo "
Usage: $comm $maxprm $cleanprm $niceprm \\
in_file n_best $optprm
For the given input file, the sequence input order is jumbled (up to maxjumble
times) until the same best tree is found n_best times. The output files are
then reduced to a summary of the scores produced by jumbling, and one example
of the best tree.
The jumble option is included by the script and should not be specified by the
user or in the data file. Additional fastDNAml program options are enclosed in
quotes, and separated by vertical bars (|).
Flags and parameters:
in_file -- name of the input data file
n_best -- input order is jumbled (up to maxjumble times) until same tree
is found n_best times
$maxflag maxjumble -- maximum attempts at replicating inferred tree
(Default=10)
$niceflag nicevalue -- run fastDNAml with specified nice value (Default=10)
$cleanflag -- inhibits cleanup of the output files
"
exit
fi
if test $cleanUp -ne 0; then cleanflag=""; fi
if test -f "$1"; then
root=`echo "$1" | sed -e 's/\.phylip$//' -e 's/\.phy$//'`; in="$1"
elif test -f "$1.phy"; then
root="$1"; in="$1.phy"
elif test -f "$1.phylip"; then
root="$1"; in="$1.phylip"
else
echo "$comm: Unable to find input file: $1"; exit
fi
out=`echo "$root" | sed -e 's&^.*/&&'`
# Don't clobber an existing file
if test $cleanUp -ne 0 -a \( -f "$out.tree" -o -f "$out.out" \); then
echo ""
echo "$comm: File(s) with the name(s) $out.out and/or $out.tree"
echo "already exist and would be clobbered by 'cleaning' the jumble output"
echo "files. Move them to a new name and try again."
echo ""
exit
fi
# Loop over jumble orders:
while
if test $cleanUp -ne 0 -a -f "$out.summary"; then
echo ""
echo "$comm: Jumbling stopped by existence of summary file:"
echo "$out.summary"
echo ""
jumbles=0
nBest=0
nJumble=0
elif test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -gt 0; then
nJumble=`grep '^Ln Likelihood' $out.[0-9]* /dev/null | wc -l`
nBest=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
sed -e 's/^.*:Ln Likelihood =\(.*\)$/\1/g' | sort -nr +0 |
awk 'BEGIN{c=0} NR==1{b=$1-0.001} $1>=b{c++} END{print c}'`
else
nBest=0
nJumble=0
fi
test $nBest -lt $2 -a $nJumble -lt $jumbles
do
eval "jumble < $in $opts |
nice -$nice out.PID fastDNAml $out" >/dev/null || exit
done
if test $cleanUp -ne 0; then clean_jumbles "$out"; fi
|
