test_rmats

#!/bin/bash

function set_script_dir() {
  local REL_SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})" || return 1
  cd "${REL_SCRIPT_DIR}" || return 1
  SCRIPT_DIR="$(pwd)" || return 1
}

function write_test_config() {
  local TEST_BASE_DIR="${SCRIPT_DIR}/tests"
  local TEST_CONFIG="${TEST_BASE_DIR}/test_config.py"
  local RUN_RMATS="${SCRIPT_DIR}/run_rmats"
  local CP_WITH_PREFIX="${SCRIPT_DIR}/cp_with_prefix.py"
  local PREPARE_STAT_INPUTS="${SCRIPT_DIR}/rMATS_P/prepare_stat_inputs.py"

  echo "TEST_BASE_DIR = '${TEST_BASE_DIR}'" > "${TEST_CONFIG}" || return 1
  echo "RMATS_COMMAND = '${RUN_RMATS}'" >> "${TEST_CONFIG}" || return 1
  echo "CP_WITH_PREFIX = '${CP_WITH_PREFIX}'" >> "${TEST_CONFIG}" || return 1
  echo "PREPARE_STAT_INPUTS = '${PREPARE_STAT_INPUTS}'" \
       >> "${TEST_CONFIG}" || return 1
}

function create_and_activate_conda_env() {
  local CONDA_ENV_PATH="${SCRIPT_DIR}/conda_envs/test_rmats"

  conda create --prefix "${CONDA_ENV_PATH}" || return 1
  conda activate "${CONDA_ENV_PATH}" || return 1
}

function install_dependencies() {
  conda install -c conda-forge -c bioconda python=3.8 samtools=1.9 || return 1
}

function main() {
  set_script_dir || return 1
  source "${SCRIPT_DIR}/setup_environment.sh" || return 1

  write_test_config || return 1
  create_and_activate_conda_env || return 1
  install_dependencies || return 1

  export PYTHONPATH="${SCRIPT_DIR}" || return 1

  if [[ "$#" -eq 0 ]]; then
    python "${SCRIPT_DIR}/tests/runner.py" || return 1
  else
    # run a specific test file if passed as an argument:
    # ./test_rmats tests/variable_read_length/tests.py
    python "$1" || return 1
  fi

  conda deactivate || return 1
}

main "$@"