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Work around the missing source name in partial SDRF file #6

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Work around the missing source name in partial SDRF file #6

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4 changes: 3 additions & 1 deletion ParsingModule.py
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Original file line number Diff line number Diff line change
Expand Up @@ -376,7 +376,9 @@ def convert_df(df):
factor_value_cols = sorted([i for i in cols if i.startswith("factor")])
#get all columns that don't start with "characteristic" or "comment"
other_cols = [i for i in cols if i not in characteristic_cols and i not in comment_cols and i not in factor_value_cols and i not in ["source name"]]
#reorder the columns
#reorder the columns, add "source name" if it is missing
if "source name" not in df:
df["source name"] = ""
new_cols = ["source name"] + characteristic_cols + other_cols + comment_cols + factor_value_cols
df = df[new_cols]
#if a column name contains _ followed by a number, remove the underscore and the number
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