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| author | Alexander_Kabui | 2025-01-29 13:49:01 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2025-02-06 12:43:15 +0300 |
| commit | a3052281899a96b6be853582e9bdc5486a78a803 (patch) | |
| tree | 4eed1d66e6ebd853a7a7ae159e7d8256e3d20d06 | |
| parent | cc24208b4eb0bb8231c636cd95a50ce327b72351 (diff) | |
| download | genenetwork3-a3052281899a96b6be853582e9bdc5486a78a803.tar.gz | |
refactor: Rename pheno_map to physical_map .
| -rw-r--r-- | gn3/api/rqtl2.py | 4 | ||||
| -rw-r--r-- | gn3/computations/rqtl2.py | 2 | ||||
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 2 |
3 files changed, 4 insertions, 4 deletions
diff --git a/gn3/api/rqtl2.py b/gn3/api/rqtl2.py index fb6363e..b584b12 100644 --- a/gn3/api/rqtl2.py +++ b/gn3/api/rqtl2.py @@ -23,9 +23,9 @@ def compute(): if not valid: return jsonify({"Error" : error}), 400 # Provide atleast one of this data entries. - if "pheno_map_data" not in data and "geno_map_data" not in data: + if "physical_map_data" not in data and "geno_map_data" not in data: return jsonify({ "Error":"You need to Provide\ - Either the Pheno map or Geno Map data"}), 400 + Either the Physical map or Geno Map data of markers"}), 400 run_id = request.args.get("id", "output") # prepare necessary files and dir for computation (workspace_dir, input_file, diff --git a/gn3/computations/rqtl2.py b/gn3/computations/rqtl2.py index f1e3cfd..0fd8a7f 100644 --- a/gn3/computations/rqtl2.py +++ b/gn3/computations/rqtl2.py @@ -16,7 +16,7 @@ def generate_rqtl2_files(data, workspace_dir): "geno_file": "geno_data", "pheno_file": "pheno_data", "geno_map_file": "geno_map_data", - "pheno_map_file": "pheno_map_data", + "physical_map_file": "physical_map_data", "phenocovar_file": "phenocovar_data", } parsed_files = {} diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index accf3fa..69606b2 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -100,7 +100,7 @@ generate_cross_object <- function(control_file_path, json_data) { geno_file = json_data$geno_file, pheno_file = json_data$pheno_file, gmap_file = json_data$geno_map_file, - pmap_file = json_data$pheno_map_file, + pmap_file = json_data$physical_map_file, phenocovar_file = json_data$phenocovar_file, geno_codes = json_data$geno_codes, alleles = json_data$alleles, |