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|
#!/bin/bash
# Usage $0
# Tests that querying slow5 index files matches the expected output.
# Note:
#
# - Don't move this file from "slow5/tests/".
# Requires subdirectory "data/" with testing dataset(s),
# and "slow5tools" executable in parent directory.
#
# - Expects testing datasets with the following structure:
# - dataset/
# |- expected.slow5
# |- expected.slow5.s5i
# Relative path to "slow5/tests/"
REL_PATH="$(dirname $0)/"
# Folder containing testing datasets
DATA_DIR="$REL_PATH/data"
# Ensure data directory exists
if [ ! -d $DATA_DIR ]; then
echo "ERROR: Missing data directory \""$REL_PATH"/"$DATA_DIR"\""
echo "Exiting"
exit 1
fi
# Path to slow5tools
SLOW5TOOLS_PATH="$REL_PATH/../slow5tools"
# Ensure slow5tools exists
if [ ! -f $SLOW5TOOLS_PATH ]; then
echo "ERROR: Missing slow5tools \""$REL_PATH"/"$SLOW5TOOLS_PATH"\""
echo "Exiting"
exit 1
fi
CMD_SLOW5_IDX_QUERY="extract"
# File name of expected SLOW5 output
SLOW5_EXPECTED="expected.slow5"
declare -i ret=0
declare -i total_tests=0
declare -i total_passed=0
# Iterate through each testset
for testset in $DATA_DIR/*; do
echo "$testset"
declare -i n_lines=$(wc -l < "$testset/$SLOW5_EXPECTED")
declare -i n_tests=$(( $n_lines / 10 ))
if [ $n_tests -lt 5 ]; then
n_tests=5
fi
total_tests+=$n_tests
echo Testing $n_tests reads
echo ""
for i in $(seq 1 $n_tests); do
declare -i rand_line=$(( 3 + RANDOM % ($n_lines - 3) )) # TODO change to check for #
rand_read="$(sed "${rand_line}q;d" "$testset/$SLOW5_EXPECTED")"
rand_readid="$(echo "$rand_read" | cut -f1)"
query_read="$("$SLOW5TOOLS_PATH" $CMD_SLOW5_IDX_QUERY "$testset/$SLOW5_EXPECTED" "$rand_readid" 2>/dev/null)"
if diff <(echo "$query_read") <(echo "$rand_read") 2>&1 >/dev/null; then
total_passed+=1
else
ret=1
echo -e "failure
--READ-ID------------------------
$rand_readid
---------------------------------
"
fi
done
done
if [ $ret -eq 0 ]; then
echo "PASSED $total_passed/$total_tests"
else
echo "FAILED $total_passed/$total_tests"
fi
exit $ret
|
