general.py

# valid data usage policies

import re

"""
Null Constant definitions
"""
NA_STRING = "NA"
null_values_list = [
    "nan",
    "na",
    "none",
    "",
    "undefined",
    "n/a",
    "null",
    "nil",
    "-",
]
# enforce the assumption that these are all lowercase values
assert all(s.lower() == s for s in null_values_list)

# add the NA_STRING only if it's not already in the list
if NA_STRING.lower() not in null_values_list:
    null_values_list.append(NA_STRING.lower())
null_values_list.sort()

null_values_re = re.compile(
    r"^\s+$|" + "|".join(f"^{s}$" for s in null_values_list if len(s)),
    flags=re.IGNORECASE,
)

readable_null_values_list = [f"{s}" for s in null_values_list] + ["whitespace"]

hgvs_nt_column = "hgvs_nt"
hgvs_splice_column = "hgvs_splice"
hgvs_pro_column = "hgvs_pro"
guide_sequence_column = "guide_sequence"
hgvs_columns = sorted([hgvs_nt_column, hgvs_pro_column, hgvs_splice_column])
meta_data = "meta_data"
score_columns = "score_columns"
count_columns = "count_columns"
variant_score_data = "score_data"
variant_count_data = "count_data"
required_score_column = "score"

multi_value_keys = ["molecular mechanism assessed"]
calibration_variant_column_name = "variant_urn"
calibration_class_column_name = "class_name"

valid_dataset_columns = [score_columns, count_columns]
valid_variant_columns = [variant_score_data, variant_count_data]

variant_to_score_set_column = {
    variant_score_data: score_columns,
    variant_count_data: count_columns,
}
score_set_to_variant_column = {v: k for k, v in variant_to_score_set_column.items()}