diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/ctl.py | 4 | ||||
| -rw-r--r-- | gn3/computations/wgcna.py | 6 |
2 files changed, 5 insertions, 5 deletions
diff --git a/gn3/computations/ctl.py b/gn3/computations/ctl.py index f881410..af1c508 100644 --- a/gn3/computations/ctl.py +++ b/gn3/computations/ctl.py @@ -3,7 +3,7 @@ import json from gn3.commands import run_cmd from gn3.computations.wgcna import dump_wgcna_data -from gn3.computations.wgcna import compose_wgcna_cmd +from gn3.computations.wgcna import compose_rscript_cmd from gn3.computations.wgcna import process_image from gn3.settings import TMPDIR @@ -13,7 +13,7 @@ def call_ctl_script(data): """function to call ctl script""" data["imgDir"] = TMPDIR temp_file_name = dump_wgcna_data(data) - cmd = compose_wgcna_cmd("ctl_analysis.R", temp_file_name) + cmd = compose_rscript_cmd("ctl_analysis.R", temp_file_name) cmd_results = run_cmd(cmd) with open(temp_file_name, "r", encoding="utf-8") as outputfile: diff --git a/gn3/computations/wgcna.py b/gn3/computations/wgcna.py index c985491..01aaedb 100644 --- a/gn3/computations/wgcna.py +++ b/gn3/computations/wgcna.py @@ -55,17 +55,17 @@ def process_image(image_loc: str) -> bytes: return b"" -def compose_wgcna_cmd(rscript_path: str, temp_file_path: str): +def compose_rscript_cmd(rscript_path: str, temp_file_path: str): """function to componse wgcna cmd""" # (todo):issue relative paths to abs paths - cmd = f"Rscript ./scripts/{rscript_path} {temp_file_path}" + cmd = f'"Rscript ./scripts/{rscript_path} {temp_file_path}"' return cmd def call_wgcna_script(rscript_path: str, request_data: dict): """function to call wgcna script""" generated_file = dump_wgcna_data(request_data) - cmd = compose_wgcna_cmd(rscript_path, generated_file) + cmd = compose_rscript_cmd(rscript_path, generated_file) # stream_cmd_output(request_data, cmd) disable streaming of data |