CeleScope tests

Please note that these data are for testing purposes only. Some of the data are artificially generated.

1. Get test data and scripts.

mkdir test_dir
cd test_dir
git clone https://github.com/singleron-RD/celescope_test_data.git
git clone https://github.com/singleron-RD/celescope_test_script.git

If github is blocked, an alternate repo(gitee) is available.

mkdir test_dir
cd test_dir
git clone https://gitee.com/singleron-rd/celescope_test_data.git
git clone https://gitee.com/singleron-rd/celescope_test_script.git

2. Modify arguments

• rna

celescope_test_script/rna/run_shell.sh Change --genomeDir to the human genomeDir path.

• dynaseq

celescope_test_script/dynaseq/run_shell.sh Change --genomeDir to the mouse genomeDir path.

• snp

celescope_test_script/snp/run_shell.sh Change --genomeDir to the human genomeDir path.

• capture_virus

celescope_test_data contains the EBV fasta. You can generate a EBV genomeDir by using mkref.sh under celescope_test_data/capture_virus/EBV_genome .

celescope_test_script/capture_virus/run_shell.sh Change --virus_genomeDir to the EBV genomeDir path.

3. Run pytest

• Install pytest

pip install pytest

• Run some tests

cd celescope_test_script
python -m pytest -s test_multi.py --assays tag,vdj

• Run all tests

cd celescope_test_script
python -m pytest -s test_multi.py