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|
#!/bin/sh
#set -e -x
usage()
{
echo "Usage: $0 minlength inputfile"
}
checkerror()
{
$1
if test $? -ne 0
then
echo "failure: ${1}"
exit 1
fi
}
cleanhashlines()
{
TMPFILE=`mktemp TMP.XXXXXX` || exit 1
sed -e '/^#/d' -e 's/[ ][ ]*/ /g' $1 > ${TMPFILE}
mv ${TMPFILE} $1
}
sortlines()
{
TMPFILE=`mktemp TMP.XXXXXX` || exit 1
sort -n $1 > ${TMPFILE}
mv ${TMPFILE} $1
}
extractlines()
{
TMPFILE=`mktemp TMP.XXXXXX` || exit 1
/sw/bin/gawk '/.*/ {print $1 " " $3 " " $4 " " $5 " " $7}' $1 > ${TMPFILE}
mv ${TMPFILE} $1
}
if test $# -ne 2
then
usage
exit 1
fi
minlength=$1
filename=$2
GTDIR=/Users/stefan/genometools
checkerror "${GTDIR}/bin/gt suffixerator -db ${filename} -indexname sfxidx -dna -suf -tis -lcp -pl"
checkerror "${GTDIR}/bin/gt repfind -l ${minlength} -r -ii sfxidx" > result.gt
cleanhashlines result.gt
extractlines result.gt
sortlines result.gt
checkerror "/Users/stefan/bin-ops/i686-apple-darwin/repfind.x -allmax -l ${minlength} -r -noevalue -nodistance $filename" > result.rep
cleanhashlines result.rep
sortlines result.rep
checkerror "diff -w result.rep result.gt"
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