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#! /bin/bash
#
# template-test
#
#
# Part of TREE-PUZZLE 5.2 (July 2004)
#
# (c) 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler
# (c) 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer,
# M. Vingron, and Arndt von Haeseler
# (c) 1995-1999 by Korbinian Strimmer and Arndt von Haeseler
#
# All parts of the source except where indicated are distributed under
# the GNU public licence. See http://www.opensource.org for details.
#
# ($Id$)
#
fname=`echo $0 | sed 's/.*\///'`
GENERATE=0
TESTTYPE="Testing: "
if test 0 -ne $#
then
case "$1" in
-g*)
GENERATE=1
TESTTYPE="Generating: "
;;
*)
echo "Usage: $fname [-g] "
echo
echo " Test a TREE-PUZZLE scenario."
echo " With -g no test is performed, but the "
echo " template for a future test is created."
echo
exit 1
;;
esac
fi
##########################################################################
TEST_PREF=`echo $fname | sed s/\.test//`
INUTREE=${TEST_PREF}.trees
INCTREE=${TEST_PREF}.ctrees
PARAMS=${TEST_PREF}.param
# default
DATA=nucl
INFILE=${TEST_PREF}.${DATA}
INFILESOURCE=../data/marswolf.n
INUTREESOURCE=../data/marswolf.trees
INCTREESOURCE=../data/marswolf.ctrees
#
# data type
#
case "$TEST_PREF" in
*-nucl)
TESTTYPE="${TESTTYPE}nucleotide data"
DATA=nucl
INFILE=${TEST_PREF}.${DATA}
INFILESOURCE=../data/marswolf.n
INUTREESOURCE=../data/marswolf.trees
INCTREESOURCE=../data/marswolf.ctrees
echo d > $PARAMS
case "$TEST_PREF" in
*-hky*)
TESTTYPE="${TESTTYPE}, HKY"
;;
*-tn*)
TESTTYPE="${TESTTYPE}, TN"
echo m >> $PARAMS
;;
*-gtr*)
TESTTYPE="${TESTTYPE}, TN"
echo m >> $PARAMS
echo m >> $PARAMS
;;
*-sh*)
TESTTYPE="${TESTTYPE}, SH"
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
;;
*)
TESTTYPE="${TESTTYPE}, default model"
esac
;;
*-prot)
TESTTYPE="${TESTTYPE}protein data"
DATA=prot
INFILE=${TEST_PREF}.${DATA}
INFILESOURCE=../data/globin.a
INUTREESOURCE=../data/globin.trees
INCTREESOURCE=../data/globin.ctrees
echo d > $PARAMS
echo d >> $PARAMS
case "$TEST_PREF" in
*-dayhoff*)
TESTTYPE="${TESTTYPE}, Dayhoff"
echo m >> $PARAMS
;;
*-jtt*)
TESTTYPE="${TESTTYPE}, JTT"
echo m >> $PARAMS
echo m >> $PARAMS
;;
*-mtrev*)
TESTTYPE="${TESTTYPE}, mtREV"
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
;;
*-blosum*)
TESTTYPE="${TESTTYPE}, BLOSUM"
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
;;
*-vt*)
TESTTYPE="${TESTTYPE}, VT"
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
;;
*-wag*)
TESTTYPE="${TESTTYPE}, WAG"
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
echo m >> $PARAMS
;;
*)
TESTTYPE="${TESTTYPE}, default model"
esac
;;
*-bin)
TESTTYPE="${TESTTYPE}binary data"
DATA=bin
INFILE=${TEST_PREF}.${DATA}
INFILESOURCE=../data/primates.b
INUTREESOURCE=../data/primates.trees
INCTREESOURCE=../data/primates.ctrees
echo d > $PARAMS
echo d >> $PARAMS
echo d >> $PARAMS
;;
*)
TESTTYPE="${TESTTYPE}default data, default model"
;;
esac
case "$TEST_PREF" in
*-clock*)
TESTTYPE="${TESTTYPE}, clock"
echo z >> $PARAMS
;;
esac
case "$TEST_PREF" in
*-rhet4*)
TESTTYPE="${TESTTYPE}, rate heterogeneity (4 rates)"
echo w >> $PARAMS
echo c >> $PARAMS
echo 4 >> $PARAMS
;;
*-rhet*)
TESTTYPE="${TESTTYPE}, rate heterogeneity"
echo w >> $PARAMS
;;
esac
CHECK_PREF=check-$INFILE
case "$TEST_PREF" in
qp-*)
TESTTYPE="${TESTTYPE}, quartet puzzling"
cp $INFILESOURCE $INFILE
RESULT_PREF=$INFILE
echo y >> $PARAMS
echo; echo "$TESTTYPE ($TEST_PREF)"
../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1
;;
lm-*)
TESTTYPE="${TESTTYPE}, likelihood mapping"
cp $INFILESOURCE $INFILE
RESULT_PREF=$INFILE
echo b >> $PARAMS
echo y >> $PARAMS
echo; echo "$TESTTYPE ($TEST_PREF)"
../src/puzzle$EXEEXT -randseed1001 ${INFILE} < $PARAMS > ${INFILE}.out 2>&1
;;
ut-*)
TESTTYPE="${TESTTYPE}, user tree evaluation"
cp $INFILESOURCE $INFILE
cp $INUTREESOURCE $INUTREE
RESULT_PREF=$INUTREE
echo y >> $PARAMS
echo; echo "$TESTTYPE ($TEST_PREF)"
../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INUTREE} < $PARAMS > ${INFILE}.out 2>&1
;;
cons-*)
TESTTYPE="${TESTTYPE}, consensus construction"
cp $INFILESOURCE $INFILE
cp $INCTREESOURCE $INCTREE
RESULT_PREF=$INCTREE
echo k >> $PARAMS
echo y >> $PARAMS
echo; echo "$TESTTYPE ($TEST_PREF)"
../src/puzzle$EXEEXT -randseed1001 ${INFILE} ${INCTREE} < $PARAMS > ${INFILE}.out 2>&1
;;
*)
echo; echo "$TESTTYPE ($TEST_PREF)"
echo UNKNOWN analysis type: test ignored
exit 77
;;
esac
if test $GENERATE == 1; then
cat ${RESULT_PREF}.puzzle \
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed "s/$VERSION//g" \
> check-${TEST_PREF}
exit 0
else
cat ${RESULT_PREF}.puzzle \
| grep -v "^Date and time" \
| grep -v "^Runtime (" \
| sed "s/$VERSION//g" \
> ${RESULT_PREF}.clean
diff ${RESULT_PREF}.clean check-${TEST_PREF}
result=$?
exit $result
fi
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