runcheck

来自「EM算法的改进」· 代码 · 共 220 行

#!/bin/sh

# runcheck - for testing of meme and mast
#
# $Id: runcheck 1339 2006-09-21 19:46:28Z tbailey $
#
# $Log$
# Revision 1.7  2006/03/08 20:50:11  nadya
# merge chamges from v3_5_2 branch
#
# Revision 1.6.4.2  2006/01/24 02:24:29  nadya
# EXT is obsoleted by using printf()
#
# Revision 1.6.4.1  2006/01/24 02:04:55  nadya
# source meme_config to set needed environment
# make output table-like
#
# Revision 1.6  2005/10/07 02:54:28  nadya
# clean debugging output, fix typo
#
# Revision 1.5  2005/10/04 20:03:23  nadya
# changes to accommodate sh on solaris:
# substitute array with awk parsing and  initialize err.
#
# Revision 1.4  2005/10/04 00:02:04  nadya
# change to "-f", the option "-e" does not run solaris
#
# Revision 1.3  2005/10/02 05:09:39  nadya
# add extension ".bin" to executables names for meme and mast
#
# Revision 1.2  2005/09/01 00:42:05  nadya
# call executables from $topdir befiore they are installed
# update sed regexpr
#
# Revision 1.1  2005/08/31 04:51:55  nadya
# create script and target for "make check"
#

# set meme environment
top=`pwd`/.. 
MEME_DIRECTORY="$top"
export MEME_DIRECTORY
etcdir=$top/etc
testdir=$top/tests
make_logodds=$top/scripts/make_logodds
meme=$top/src/meme.bin
mast=$top/src/mast.bin
conf=$top/scripts/meme_config

if [ ! -f $make_logodds ] ; then
    echo "$make_logodds does not exist"
    echo "Run 'make' before running 'make check'"
    exit 1
fi

if [ ! -x $meme ] ; then
    echo "$meme does not exist or is not executable"
    echo "Run 'make' before running 'make check'"
    exit 1
fi

if [ ! -x $mast ] ; then
    echo "$mast does not exist or is not executable"
    echo "Run 'make' before running 'make check'"
    exit 1
fi

if [ -f $conf ] ; then
    . $conf
else
    echo "$conf does not exist"
    echo "Run 'make' before running 'make check'"
    exit 1
fi


####################################################################
#                      define functions 
####################################################################
# run mast tests 
func_run_mast () {
    echo ""
    echo  "              Mast test for "
    echo  "    ---------------------------------"
    echo  "      Dataset       Model     result " 
    echo  "    ---------------------------------"

    for mod in $models
    do
        memefile=meme.$dset.$mod$suffix
        mastfile=mast.$dset.$mod$suffix
        logodds=$dirout/logodds.$$

        info=`perl $make_logodds $dir/$memefile $logodds`
        alphabet=`echo $info | awk '{print $1}'`
        vardb=`echo $info | awk '{print $2}'`
        database=$dir/`basename $vardb`

        params="-nostatus -logodds $logodds -alphabet $alphabet -mf $dir/$memefile"
        params="$params -database $database -df $database"
        $mast "mast $memefile" $params > $dirout/$mastfile
        func_diff $mastfile 
    done
}

# run meme tests 
func_run_meme () {
    echo ""
    echo  "              Meme test for "
    echo  "    ---------------------------------"
    echo  "      Dataset       Model     result " 
    echo  "    ---------------------------------"
    for mod in $models
    do
        memefile=meme.$dset.$mod$suffix
        $meme $pargs $dir/$dset.s -mod $mod $params > $dirout/$memefile
        func_diff $memefile 
    done
}

# remove lines specified by regexpr from the file
# takes a filename as an argument
func_sed () {
    e1="/Release date/d"
    e2="/http:/d"
    e3="/MOTIFS/d"
    e4="/Time/d"
    e5="/CPU:/d"
    e6="/DATAFILE=/d"
    e7="/DATABASE/d"
    e8="/command: /d"
    e9="/Background letter frequencies/d"
    e10="/Last updated/d"
    sed -e "$e1" -e "$e2" -e "$e3" -e "$e4" -e "$e5" \
        -e "$e6" -e "$e7" -e "$e8" -e "$e9" -e "$e10" $1 > $1.sed
}

# checks two files for differences.  Arguments - a filename
# and a string containing dataset and model info to print.
func_diff () {
    f1=$dir/$1      # first file
    f2=$dirout/$1   # second file

    # string to print
	str=`echo $dset $mod | awk '{printf("    %-16s%-8s  ",$1,$2)}'`

    if [ ! -f  $f1 ]; then
        echo "File $f1 does not exist, can't compare output"
        echo "$str" "SKIPPED"
        return 
    fi
    if [ ! -f  $f2 ]; then
        echo "File $f2 does not exist, can't compare output"
        echo "$str" "SKIPPED"
        return 
    fi
    func_sed $f1 
    func_sed $f2 
    num=`diff $f1.sed $f2.sed | wc -l`
    status=$?
    if [ $status -eq 0 -a  $num -eq 0 ]; then
        echo "$str" "OK"
    else
        echo "$str" "FAIL"
        err=1
    fi
    return 
}

# initializes tests parameters
func_set () {
    dset="crp0"
    models="oops zoops tcm"
    params="-dna -revcomp -nostatus -nmotifs 2 -minw 8"
    dir=$top/tests
    dirout=$top/tests/results
    if [ ! -d $dirout ]; then
        cmd=`mkdir $dirout`
        status=$?
        if [ $status -eq 1 ] ; then 
            exit 1
        fi
    fi
    err=0
}

# removes temp output files
func_clean () {
    /bin/rm -rf $dir/*.sed $dirout/*.sed $dirout/logodds.*
    if [ ! $err ] ; then
        /bin/rm -rf $dirout
    fi
    echo 
}


####################################################################
#             check command line arguments and run tests
####################################################################
# check arguments
while test $# -gt 0; do
    case "$1" in
    -p)
        shift
        procs=$1
        pargs="-p $1"
        suffix=".$1"
        ;;
    esac
    shift
done

# run tests
func_set 
func_run_meme
func_run_mast
func_clean

exit $err