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Change path of cleaned features in Snakefile

pull/95/head
Meng Li 2020-05-15 18:10:36 -04:00
parent 6e99e69f8c
commit 12302a9486
1 changed files with 12 additions and 2 deletions
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14
Snakefile
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@ -83,11 +83,21 @@ rule all:
expand("data/processed/data_for_population_model/{source}_{day_segment}_original.csv",
source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
expand("data/processed/{pid}/data_for_individual_model/{source}_{day_segment}_clean.csv",
expand("data/processed/{pid}/data_for_individual_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_clean.csv",
pid = config["PIDS"],
rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
expand("data/processed/data_for_population_model/{source}_{day_segment}_clean.csv",
expand("data/processed/data_for_population_model/{rows_nan_threshold}|{cols_nan_threshold}_{days_before_threshold}|{days_after_threshold}_{cols_var_threshold}/{source}_{day_segment}_clean.csv",
rows_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["ROWS_NAN_THRESHOLD"],
cols_nan_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_NAN_THRESHOLD"],
days_before_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_BEFORE_THRESHOLD"],
days_after_threshold = config["PARAMS_FOR_ANALYSIS"]["PARTICIPANT_DAYS_AFTER_THRESHOLD"],
cols_var_threshold = config["PARAMS_FOR_ANALYSIS"]["COLS_VAR_THRESHOLD"],
source = config["PARAMS_FOR_ANALYSIS"]["SOURCES"],
day_segment = config["PARAMS_FOR_ANALYSIS"]["DAY_SEGMENTS"]),
expand("data/processed/data_for_population_model/demographic_features.csv"),