28 lines
1.2 KiB
Python
28 lines
1.2 KiB
Python
import pandas as pd
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import numpy as np
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pid = snakemake.params["pid"]
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summarised = snakemake.params["summarised"]
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targets_ratio_threshold = snakemake.params["targets_ratio_threshold"]
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targets_value_threshold = snakemake.params["targets_value_threshold"]
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participant_info = pd.read_csv(snakemake.input["participant_info"])
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if summarised == "summarised":
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targets = pd.DataFrame(columns=["pid", "target"])
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if not participant_info.empty:
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cesds = participant_info.loc[0, ["preop_cesd_total", "inpatient_cesd_total", "postop_cesd_total", "3month_cesd_total"]]
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# targets: 1 => 50% (ceiling) or more of available CESD scores were 16 or higher; 0 => otherwise
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num_threshold = int((cesds.count() + 1) * targets_ratio_threshold)
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target = 1 if cesds.apply(lambda x : 1 if x >= targets_value_threshold else 0).sum() >= num_threshold else 0
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targets.loc[0, :] = [pid, target]
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elif summarised == "notsummarised":
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targets = participant_info[["local_date", "target"]]
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targets.insert(0, "pid", pid)
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else:
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raise ValueError("SUMMARISED parameter in config.yaml can only be 'summarised' or 'notsummarised'")
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targets.to_csv(snakemake.output[0], index=False)
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