diff options
| -rw-r--r-- | scripts/load_phenotypes_to_db.py | 16 |
1 files changed, 11 insertions, 5 deletions
diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py index d31ade6..533b0e3 100644 --- a/scripts/load_phenotypes_to_db.py +++ b/scripts/load_phenotypes_to_db.py @@ -49,21 +49,27 @@ def save_phenotypes( """Read `phenofiles` and save the phenotypes therein.""" logger.info("Saving new phenotypes.") logger.debug("Processing %s 'pheno' files.", len(phenofiles)) - phenofiles = control_data["pheno"] + ## TODO: Replace with something like this: ## + # phenofiles = control_data["phenocovar"] + control_data.get( + # "gn-metadata", {}).get("pheno", []) + # + # This is meant to load (and merge) data from the "phenocovar" and + # "gn-metadata -> pheno" files into a single collection of phenotypes. + phenofiles = control_data["phenocovar"] if len(phenofiles) <= 0: return tuple() - if control_data["pheno_transposed"]: + if control_data["phenocovar_transposed"]: logger.info("Undoing transposition of the files rows and columns.") phenofiles = ( transpose_csv_with_rename( _file build_line_splitter(control_data) build_line_joiner(control_data)) - for _file in control_data["pheno"]) + for _file in control_data["phenocovar"]) - _headers = rqtl2.read_csv_file_headers(control_data["pheno"][0], - control_data["pheno_transposed"], + _headers = rqtl2.read_csv_file_headers(control_data["phenocovar"][0], + control_data["phenocovar_transposed"], control_data["sep"], control_data["comment.char"]) return create_new_phenotypes( |