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Try to stop outputting files if not displayed or built #352

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d549a04
try to stop outputting files if not displayed or built
emmahodcroft Oct 17, 2022
9c847d2
revert changes and ad early check
MoiraZuber2 Oct 26, 2022
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13 changes: 12 additions & 1 deletion scripts/cluster_analysis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,16 @@ def print_all_clus_alerts(key):
else:
print(f"Not found. Options are: {clusters.keys()}")

print("These clusters will be run: ", clus_to_run)
print("These clusters will be run: ", clus_to_run, "\n")

removed = False
for clus in clus_to_run:
if clusters[clus]["type"] == "do_not_display" and not clusters[clus]["nextstrain_build"]:
print(f"Remark: cluster {clus} has type 'do_not_display' and nextstrain_build=False -> Will be automatically removed from this run (maybe consider commenting out this cluster?)")
clus_to_run.remove(clus)
removed = True
if removed:
print("\nThese clusters will be run: ", clus_to_run, "\n")

# division: collect division info for USA and Switzerland
division = False
Expand Down Expand Up @@ -692,6 +701,8 @@ def print_all_clus_alerts(key):
print(f"No summary written out for cluster {clus} (no sequences assigned to this cluster).")
continue

nextstrain_run = clusters[clus]['nextstrain_build']
build_type = clusters[clus]['type']
clus_build_name = clus_data_all[clus]["build_name"]
table_file = f"{tables_path}{clus_build_name}_table.tsv"
ordered_country = pd.DataFrame.from_dict(clus_data_all[clus]["summary"], orient="index").sort_values(by=["first_seq", "last_seq"])
Expand Down