diff options
| -rw-r--r-- | gn3/api/rqtl.py | 2 | ||||
| -rw-r--r-- | gn3/computations/gemma.py | 11 |
2 files changed, 12 insertions, 1 deletions
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py index 36bc3da..0a380a4 100644 --- a/gn3/api/rqtl.py +++ b/gn3/api/rqtl.py @@ -9,7 +9,7 @@ from flask import request from gn3.debug import __pk__ from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, \ process_rqtl_pairscan, process_perm_output -from gn3.fs_helpers import assert_paths_exist +from gn3.computations.gemma import assert_paths_exist rqtl = Blueprint("rqtl", __name__) diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py index 2c367ff..f97fa6d 100644 --- a/gn3/computations/gemma.py +++ b/gn3/computations/gemma.py @@ -41,6 +41,17 @@ def generate_pheno_txt_file(trait_filename: str, return f"{tmpdir}/gn2/{trait_filename}" +def assert_paths_exist(paths: ValuesView) -> bool: + """Given a list of PATHS, throw error if any of them do not exist.""" + for path in paths: + if not os.path.isfile(path): + if throw_error: + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path) + else: + return False + return True + + # pylint: disable=R0913 def generate_gemma_cmd(gemma_cmd: str, output_dir: str, |