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|
#!/bin/bash
set -e
pkg=pycoqc
CUR_DIR=`pwd`
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp ${CUR_DIR}/docs/Barcode_split/data/* -a "${AUTOPKGTEST_TMP}"
cp ${CUR_DIR}/docs/Fast5_to_seq_summary/data/* -a "${AUTOPKGTEST_TMP}"
cp ${CUR_DIR}/docs/pycoQC/data/* -a "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
gunzip -r *
rm -rf data
mkdir -p datafast5
mv *.fast5 datafast5
mv summary_sequencing.tsv datafast5
echo 'Test 1'
pycoQC \
-f Albacore-1.2.1_basecall-1D-DNA_sequencing_summary.txt \
-o results/Albacore-1.2.1_basecall-1D-DNA.html \
--quiet
echo 'PASS'
echo
echo 'Test 2'
pycoQC \
-f Guppy-2.1.3_basecall-1D-RNA_sequencing_summary.txt \
-o results/Guppy-2.1.3_basecall-1D_RNA.html \
-j results/Guppy-2.1.3_basecall-1D_RNA.json \
--quiet
echo 'PASS'
echo
echo 'Test 3'
pycoQC \
-f Guppy-2.1.3_basecall-1D-DNA_sequencing_summary.txt \
-b Guppy-2.1.3_basecall-1D_DNA_barcoding_summary.txt \
-o results/Guppy-2.1.3_basecall-1D_DNA_barcode.html \
--quiet
echo 'PASS'
echo
echo 'Test 4'
pycoQC \
-f Albacore*RNA* \
-o results/Albacore_all_RNA.html \
--report_title "All RNA runs" \
--quiet
echo 'PASS'
echo
echo 'Test 5'
pycoQC \
-f Albacore-2.1.10_basecall-1D-DNA_sequencing_summary.txt\
-o results/Albacore-2.1.10_basecall-1D-DNA.html \
--min_pass_qual 8 \
--min_pass_len 200 \
--filter_calibration \
--min_barcode_percent 10 \
--quiet
echo 'PASS'
echo
echo 'Test 6'
pycoQC --default_config > test6
diff test6 pycoQC_config.json
echo 'PASS'
echo
echo 'Test 7'
pycoQC \
-f Albacore-1.7.0_basecall-1D-DNA_sequencing_summary.txt\
-o results/Albacore-1.7.0_basecall-1D-DNA.html \
--config pycoQC_config.json \
--quiet
echo 'PASS'
echo
echo 'Test 8'
Fast5_to_seq_summary \
-f datafast5/ \
-s results/summary_sequencing.tsv
head results/summary_sequencing.tsv
echo 'PASS'
echo
echo 'Test 9'
Fast5_to_seq_summary \
-f datafast5/ \
-s results/custom_summary_sequencing.tsv \
--verbose_level 1 \
--fields mean_qscore_template called_events duration strand_score
head results/custom_summary_sequencing.tsv
echo 'PASS'
echo
echo 'Test 10'
Fast5_to_seq_summary \
-f datafast5/ \
-s results/fn_summary_sequencing.tsv \
--verbose_level 1 \
--include_path
head results/fn_summary_sequencing.tsv
echo 'PASS'
echo
echo 'Test 11'
Barcode_split \
-f 'Guppy-2.2.4-basecall-1D-DNA_sequencing_summary+barcode.txt' \
-o "results/"
echo 'PASS'
echo
echo 'Test 12'
Barcode_split \
-f "Guppy-basecall-1D-DNA_sequencing_summary.txt" \
-b "Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt" \
-o "results/" \
-v
echo 'PASS'
echo
echo "Check if files really exist"
for f in results/*
do
[ -s $f ] || exit 1
done
echo "PASS"
echo
|
