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|
#!/bin/bash
# Usage $0
# Tests that f2s matches the expected output.
# Note:
#
# - Don't move this file from "slow5/tests/".
# Requires subdirectory "data/" with testing dataset(s),
# and "slow5tools" executable in parent directory.
#
# - Expects testing datasets with the following structure:
# - dataset/
# |- expected.slow5
# |- expected.slow5.s5i
# |- expected.blow5
# |- expected.blow5.b5i
# |- fast5_files/
# |- expected_1.fast5
# |- ...
# Relative path to "slow5/tests/"
REL_PATH="$(dirname $0)/"
# Change directory to tests folder
# since filenames are output relative this directory
# and will influence test results
# TODO necessary?
cd $REL_PATH
# Folder containing testing datasets
DATA_DIR="data"
# Ensure data directory exists
if [ ! -d $DATA_DIR ]; then
echo "ERROR: Missing data directory \""$REL_PATH"/"$DATA_DIR"\""
# Change back to original directory
cd - >/dev/null
echo "Exiting"
exit 1
fi
# Path to slow5tools
SLOW5TOOLS_PATH="../slow5tools"
# Ensure slow5tools exists
if [ ! -f $SLOW5TOOLS_PATH ]; then
echo "ERROR: Missing slow5tools \""$REL_PATH"/"$SLOW5TOOLS_PATH"\""
# Change back to original directory
cd - >/dev/null
echo "Exiting"
exit 1
fi
CMD_FAST5_TO_SLOW5="f2s"
CMD_FAST5_TO_BLOW5="f2s -b"
CMD_SLOW5_IDX="index"
CMD_BLOW5_IDX="index"
# Folder name in datasets containing FAST5 files
FAST5_FOLDER="fast5_files/"
# File name of expected SLOW5 output
SLOW5_EXPECTED="expected.slow5"
# File name of actual SLOW5 output
SLOW5_ACTUAL="actual.slow5"
# File name of expected BLOW5 output
BLOW5_EXPECTED="expected.blow5"
# File name of actual BLOW5 output
BLOW5_ACTUAL="actual.blow5"
# File name of expected SLOW5 index output
SLOW5_IDX_EXPECTED="expected.slow5.s5i"
# File name of actual SLOW5 index output
SLOW5_IDX_ACTUAL="actual.slow5.s5i"
# File name of expected SLOW5 index output
BLOW5_IDX_EXPECTED="expected.blow5.b5i"
# File name of actual SLOW5 index output
BLOW5_IDX_ACTUAL="actual.blow5.b5i"
declare -i ret=0
# Iterate through each testset
for testset in $DATA_DIR/*; do
echo "$testset"
rm "$testset/$SLOW5_ACTUAL"
rm "$testset/$SLOW5_IDX_ACTUAL"
# Sort the reads but not the header
"$SLOW5TOOLS_PATH" "$CMD_FAST5_TO_SLOW5" "$testset/$FAST5_FOLDER" 2>/dev/null | awk '{if (substr($0,1,1) == "#") print $0 > "/dev/stderr"; else print $0}' 2> "$testset/$SLOW5_ACTUAL" | sort -r >> "$testset/$SLOW5_ACTUAL"
"$SLOW5TOOLS_PATH" $CMD_SLOW5_IDX "$testset/$SLOW5_ACTUAL" 2>/dev/null
if diff "$testset/$SLOW5_EXPECTED" "$testset/$SLOW5_ACTUAL" 2>&1 >/dev/null; then
echo "SUCCESS fast5 -> slow5"
else
echo "FAILED fast5 -> slow5"
ret=1
fi
if diff "$testset/$SLOW5_IDX_EXPECTED" "$testset/$SLOW5_IDX_ACTUAL" 2>&1 >/dev/null; then
echo "SUCCESS slow5 index"
else
echo "FAILED slow5 index"
ret=1
fi
rm "$testset/$BLOW5_ACTUAL"
rm "$testset/$BLOW5_IDX_ACTUAL"
"$SLOW5TOOLS_PATH" $CMD_FAST5_TO_BLOW5 "$testset/$FAST5_FOLDER" -o "$testset/$BLOW5_ACTUAL" 2>/dev/null
"$SLOW5TOOLS_PATH" "$CMD_BLOW5_IDX" "$testset/$BLOW5_ACTUAL" 2>/dev/null
if diff "$testset/$BLOW5_EXPECTED" "$testset/$BLOW5_ACTUAL" 2>&1 >/dev/null; then
echo "SUCCESS fast5 -> blow5"
else
echo "FAILED fast5 -> blow5"
ret=1
fi
if diff "$testset/$BLOW5_IDX_EXPECTED" "$testset/$BLOW5_IDX_ACTUAL" 2>&1 >/dev/null; then
echo "SUCCESS blow5 index"
else
echo "FAILED blow5 index"
ret=1
fi
echo ""
done
# Change back to original directory
cd - >/dev/null
if [ $ret -eq 0 ]; then
echo "PASSED"
else
echo "FAILED"
fi
exit $ret
|
