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plot_summary: remove deprecated retrieve_snakemake_keys function

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This commit is contained in:
martacki 2022-06-08 15:49:06 +02:00
parent 565c2cbf6f
commit cd92d8092b
1 changed files with 4 additions and 4 deletions
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8
scripts/plot_summary.py
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@ -21,7 +21,7 @@ Description
import os import os
import logging import logging
from _helpers import configure_logging, retrieve_snakemake_keys from _helpers import configure_logging
import pandas as pd import pandas as pd
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
@ -170,12 +170,12 @@ if __name__ == "__main__":
attr='', ext='png', country='all') attr='', ext='png', country='all')
configure_logging(snakemake) configure_logging(snakemake)
paths, config, wildcards, logs, out = retrieve_snakemake_keys(snakemake) config = snakemake.config
summary = wildcards.summary summary = snakemake.wildcards.summary
try: try:
func = globals()[f"plot_{summary}"] func = globals()[f"plot_{summary}"]
except KeyError: except KeyError:
raise RuntimeError(f"plotting function for {summary} has not been defined") raise RuntimeError(f"plotting function for {summary} has not been defined")
func(os.path.join(paths[0], f"{summary}.csv"), config, out[0]) func(os.path.join(snakemake.input[0], f"{summary}.csv"), config, snakemake.output[0])