diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/load_phenotypes_to_db.py | 26 |
1 files changed, 15 insertions, 11 deletions
diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py index 5027a9b..0797db5 100644 --- a/scripts/load_phenotypes_to_db.py +++ b/scripts/load_phenotypes_to_db.py @@ -94,7 +94,7 @@ def save_pheno_data( ): """Read the `datafiles` and save the data in the database.""" phenofiles = tuple( - filesdir.joinpath(_file) for file in control_data["pheno"]) + filesdir.joinpath(_file) for _file in control_data["pheno"]) if len(phenofiles) <= 0: return tuple() @@ -128,10 +128,12 @@ def save_phenotype_se( conn: mysqldb.Connection, dataidmap: dict, samples: tuple[dict, ...], - control_data: dict + control_data: dict, + filesdir: Path ): """Read the `sefiles` and save the data in the database.""" - sefiles = control_data["phenose"] + sefiles = tuple( + filesdir.joinpath(_file) for _file in control_data["phenose"]) if len(sefiles) <= 0: return tuple() @@ -142,9 +144,9 @@ def save_phenotype_se( _file, build_line_splitter(control_data), build_line_joiner(control_data)) - for _file in control_data["phenose"]) + for _file in sefiles) - _headers = rqtl2.read_csv_file_headers(control_data["phenose"][0], + _headers = rqtl2.read_csv_file_headers(sefiles[0], control_data["phenose_transposed"], control_data["sep"], control_data["comment.char"]) @@ -165,23 +167,25 @@ def save_phenotype_n( conn: mysqldb.Connection, dataidmap: dict, samples: tuple[dict, ...], - control_data: dict + control_data: dict, + filesdir: Path ): """Read the `nfiles` and save the data in the database.""" - sefiles = control_data["phenonum"] - if len(sefiles) <= 0: + nfiles = tuple( + filesdir.joinpath(_file) for _file in control_data["phenonum"]) + if len(nfiles) <= 0: return tuple() if control_data["phenonum_transposed"]: logger.info("Undoing transposition of the files rows and columns.") - sefiles = ( + nfiles = ( rqtl2.transpose_csv_with_rename( _file, build_line_splitter(control_data), build_line_joiner(control_data)) - for _file in control_data["phenonum"]) + for _file in nfiles) - _headers = rqtl2.read_csv_file_headers(control_data["phenonum"][0], + _headers = rqtl2.read_csv_file_headers(nfiles[0], control_data["phenonum_transposed"], control_data["sep"], control_data["comment.char"]) |