From 96dfc3fba3900191ab809011328d042a14d9d3f5 Mon Sep 17 00:00:00 2001 From: Laura Luebbert Date: Fri, 24 May 2024 16:31:27 -0700 Subject: [PATCH] Debugging --- gget/gget_cosmic.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gget/gget_cosmic.py b/gget/gget_cosmic.py index 226d383a..d7684858 100644 --- a/gget/gget_cosmic.py +++ b/gget/gget_cosmic.py @@ -258,7 +258,7 @@ def cosmic( ## Create copy of results formatted for further use by gget mutate if verbose: logger.info( - "Creating modified database file for use with gget mutate..." + "Creating modified mutations file for use with gget mutate..." ) if mutation_class == "cancer" or mutation_class == "cancer_example": @@ -280,7 +280,7 @@ def cosmic( # Get seq_ID and mutation columns if mutation_class == "cancer" or mutation_class == "cancer_example": - df["MUTATION_ID"] = df["MUTATION_URL"].str.extract(r"id=(\d+)") + df["MUTATION_URL"] = df["MUTATION_URL"].str.extract(r"id=(\d+)") df = df.rename( columns={ "ACCESSION_NUMBER": "seq_ID", @@ -306,6 +306,11 @@ def cosmic( mutate_csv_out = mutation_tsv_file.replace(".tsv", "_gget_mutate.csv") df.to_csv(mutate_csv_out, index=False) + if verbose: + logger.info( + f"Modified mutations file for use with gget mutate created at {mutate_csv_out}" + ) + else: # Check if 'entity' argument is valid sps = [