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|
#!/bin/sh
errorout()
{
echo $1 #> /dev/stderr
[ "$MYTMP" = "" ] || rm -r "${MYTMP}"
exit 1
}
[ $# -ne 6 ] && exit 1
SRCDIR=$1
BINDIR=$2
PROG=$3
DI=$4
MODE=$5
EXTENSION=$6
# check existence of commands
which openssl gunzip mktemp diff cat zcat zgrep > /dev/null
[ $? -eq 0 ] || errorout "Not all required programs found. Needs: openssl gunzip mktemp diff cat zcat zgrep"
SALPH=prot # actual subject alph
QALPHIN=prot # query input file alph
SALPHIN=prot # subject input file alph
case "$PROG" in "blastn")
QALPHIN=nucl
SALPH=nucl
SALPHIN=nucl
;;
"blastp")
;;
"blastx")
QALPHIN=nucl
;;
"tblastn")
SALPH=trans
SALPHIN=nucl
;;
"tblastx")
SALPH=trans
QALPHIN=nucl
SALPHIN=nucl
;;
esac
MYTMP="$(mktemp -q -d -t "$(basename "$0").XXXXXX" 2>/dev/null || mktemp -q -d)"
[ $? -eq 0 ] || errorout "Could not create tmp"
cd "$MYTMP"
[ $? -eq 0 ] || errorout "Could not cd to tmp"
gunzip < "${SRCDIR}/tests/db_${SALPHIN}.fasta.gz" > db.fasta
[ $? -eq 0 ] || errorout "Could not unzip database file"
${BINDIR}/bin/lambda_indexer -d db.fasta -di ${DI} -p ${PROG}
[ $? -eq 0 ] || errorout "Could not run the indexer"
openssl md5 * > md5sums
[ $? -eq 0 ] || errorout "Could not run md5 or md5sums"
gunzip < "${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums.gz" > md5sums.orig
[ $? -eq 0 ] || errorout "Could not unzip md5sums.orig"
[ "$(cat md5sums)" = "$(cat md5sums.orig)" ] || errorout "$(diff -u md5sums md5sums.orig)"
## INDEXER tests end here
if [ "$MODE" = "MKINDEX" ]; then
rm -r "${MYTMP}"
exit 0
fi
gunzip < "${SRCDIR}/tests/queries_${QALPHIN}.fasta.gz" > queries.fasta
[ $? -eq 0 ] || errorout "Could not unzip queries.fasta"
${BINDIR}/bin/lambda -d db.fasta -di ${DI} -p ${PROG} -q queries.fasta -t 1 --version-to-outputfile off \
-o output_${PROG}_${DI}.${EXTENSION}
[ $? -eq 0 ] || errorout "Search failed."
[ "$(openssl md5 output_${PROG}_${DI}.${EXTENSION})" = \
"$(zgrep "(output_${PROG}_${DI}.${EXTENSION})" "${SRCDIR}/tests/search_test_outfile.md5sums.gz")" ] || errorout "MD5 mismatch of output file"
rm -r "${MYTMP}"
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