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fix: allow global error flag variable to be changed inside function #138

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merged 3 commits into from
May 17, 2023
Merged

fix: allow global error flag variable to be changed inside function #138

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c3a19f0
fix: no nan in function call
ninsch3000 May 12, 2023
391ce37
fix: update global e_flag inside function
ninsch3000 May 12, 2023
1714279
fix: tag e_flag as global in ALL functions
ninsch3000 May 17, 2023
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2 changes: 1 addition & 1 deletion workflow/rules/htsinfer.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ config.setdefault("records", 100000)


# global variables
samples = pd.read_csv(config["samples"], header=0, index_col=0, sep="\t")
samples = pd.read_csv(config["samples"], header=0, index_col=0, sep="\t", keep_default_na=False)
OUT_DIR = config["outdir"]
LOG_DIR = os.path.join(OUT_DIR, "logs")
CLUSTER_LOG = os.path.join(LOG_DIR, "cluster_logs")
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11 changes: 7 additions & 4 deletions workflow/scripts/htsinfer_to_tsv.py
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Expand Up @@ -41,6 +41,7 @@ def parse_arguments():


def main():
global e_flag
# input parameters
file_list = options.file_list

Expand All @@ -49,7 +50,7 @@ def main():
samples_df = samples_df.replace(r'^\s*$', np.nan, regex=True)
# replace None
samples_df = samples_df.fillna(value=np.nan)

LOGGER.debug(f"samples_df: {samples_df}")
outfile = options.output

params_df = pd.DataFrame(columns=[
Expand Down Expand Up @@ -106,20 +107,22 @@ def main():

def should_i_flag(df, sample, param):
'''Only RAISE error if user hasn't specified value either'''

global e_flag
LOGGER.debug(f"flag before: {e_flag}")
try:
user_param = df.loc[sample,param]
except KeyError:
user_param = np.nan
if user_param is np.nan:
if np.isnan(user_param):
e_flag = True

LOGGER.debug(f"flag after: {e_flag}")
return e_flag


def htsinfer_to_zarp(sample,jparams, samples_df):
'''Translate htsinfer json output to zarp compatible row.'''

global e_flag
# need to swap filepaths?
swap_paths = False

Expand Down