/
test.sh
executable file
·79 lines (55 loc) · 2.51 KB
/
test.sh
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#!/bin/bash
set -o nounset
set -o pipefail
#path=build/bin
path=src
mkdir -p out
$path/mlat || true
# fail
$path/mlat database query out/out-fail.psl || true
small="-tileSize=6 -stepSize=2 -minScore=1"
$path/mlat $small data/ref1.fna data/query1.fna out/out-0.0.psl
$path/mlat $small -mask=lower -qMask=lower data/ref1.fna data/query1.fna out/out-0.1.psl
$path/mlat $small -trimT -trimHardA data/ref1.fna data/query1.fna out/out-0.2.psl
$path/mlat $small data/ref1.2bit:seq1:5-85 data/query1.fna out/out-0.3.psl
$path/mlat $small data/ref1.2bit:seq1:5-85 data/query1.2bit:read1.2 out/out-0.4.psl
# fail
$path/mlat -t=prot -q=prot data/ref1.2bit:seq1:5-85 data/query1.2bit out/out-fail.psl || true
$path/mlat -makeOoc=out/11.ooc data/hg38_tp53.2bit data/reads_tp53.fa out/out-1.0.psl
$path/mlat data/hg38_tp53.2bit data/reads_tp53.fa.gz out/out-1.1.psl
$path/mlat -ooc=out/11.ooc data/hg38_tp53.2bit data/reads_tp53.fa.gz out/out-1.1.psl
formats=( pslx axt maf sim4 wublast blast blast8 blast9 )
for format in ${formats[@]}; do
$path/mlat -out=${format} data/hg38_tp53.2bit data/reads_tp53.fa.gz out/out-1.1.${format}
done
$path/mlat -t=dnax -q=dnax data/hg38_tp53.2bit data/reads_tp53.fa.gz out/out-2.0.psl
$path/mlat -t=prot -q=prot data/protein_tp53.faa data/peptides_tp53.faa out/out-3.0.psl
$path/mlat -t=dnax -q=prot data/hg38_tp53.2bit data/peptides_tp53.faa out/out-4.0.psl
cd demo
./mlat-demo || true
./mlat-demo-cpp || true
./mlat-demo ../data/ref1.fna AGACGGTCGATCGGGATTCGAGGTCGA > ../out/out-5.0.tsv
./mlat-demo-cpp ../data/ref1.fna AGACGGTCGATCGGGATTCGAGGTCGA > ../out/out-5.1.tsv
./mlat-demo ../data/hg38_tp53.2bit TCATGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGATTCCATCTCAAAAAAAAAAAAAAGGCCTCCCCTGCTT > ../out/out-6.0.tsv
./mlat-demo-cpp ../data/hg38_tp53.2bit TCATGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGATTCCATCTCAAAAAAAAAAAAAAGGCCTCCCCTGCTT > ../out/out-6.1.tsv
# output should be empty
./mlat-demo ../data/ref1.fna CCCCCCCCCCCCCCCCCCCCCCCCC > ../out/out-7.0.tsv
./mlat-demo-cpp ../data/ref1.fna CCCCCCCCCCCCCCCCCCCCCCCCC > ../out/out-7.1.tsv
cd ..
$path/2bit || true
$path/2bit data/hg38_tp53.fna out/hg38_tp53.2bit
echo
echo "Checking outputs..."
echo
cases=( \
0.0.psl 0.1.psl 0.2.psl 0.3.psl 0.4.psl \
1.0.psl 1.1.psl \
1.1.pslx 1.1.axt 1.1.maf 1.1.sim4 1.1.wublast 1.1.blast 1.1.blast8 1.1.blast9 \
2.0.psl 3.0.psl 4.0.psl \
5.0.tsv 5.1.tsv 6.0.tsv 6.1.tsv 7.0.tsv 7.1.tsv \
)
for x in ${cases[@]}; do
echo "diff out/out-${x} test/test-${x}"
diff out/out-${x} test/test-${x}
done
diff <(xxd data/hg38_tp53.2bit) <(xxd out/hg38_tp53.2bit)