diff --git a/publish.py b/publish.py index b7335a4faf80ee85a861cc094371b04ab32fa9f8..bfd7301394b0e357cbee27e2d0c5886574ac1c80 100644 --- a/publish.py +++ b/publish.py @@ -9,11 +9,12 @@ def main(config): else: raise Exception("Concepts file must be '.csv' filetype") - filename = config["concepts"][:-4] - for name, concept in df.groupby("MELDB_concept"): - concept.sort_values(by="code") - concept.to_csv(os.path.join(config["output"], str(name)+".csv"), + concept = concept.sort_values(by="code") #sort rows + concept = concept.dropna(how='all', axis=1) #remove empty cols + concept = concept.reindex(sorted(concept.columns), axis=1) #sort cols alphabetically + + concept.to_csv(os.path.join(config["output"], str(name)+".csv"), #save to csv index=False ) diff --git a/run.sh b/run.sh index 85acb40421b5bac7c5ce1ebb810fafdf1a020e96..b64772d21a5e2476e544c0afd6826de0502df4aa 100644 --- a/run.sh +++ b/run.sh @@ -1,7 +1,7 @@ #! /usr/bin/bash -version="V3_2_7" -previous="V3_2_6" +version="V3_2_10" +previous="V3_2_9" python main.py -r2 PHEN_assign_v3.json CONC_summary_working.xlsx mv output/MELD_concepts_read.csv output/${version}_MELD_concepts_readv2.csv