fixed gget cosmic with -mc cancer -cv 101

pachterlab · Feb 21, 2025 · 85fb266 · 85fb266
1 parent 61073ce
commit 85fb266
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/gget/gget_cosmic.py b/gget/gget_cosmic.py
@@ -105,6 +105,8 @@ def select_reference(
         if str(cosmic_version) == "100":  # special treatment due to v2
             download_link = download_link.replace(".tar&bucket=downloads", "_v2.tar&bucket=downloads")
             tarred_folder += "_v2"
+        elif str(cosmic_version) == "101":  # special treatment due to link difference - path=grch37 instead of path=GRCh37
+            download_link = download_link.replace(f"path=GRCh{grch_version}", f"path=grch{grch_version}")
 
     elif mutation_class == "cell_line":
         download_link = f"https://cancer.sanger.ac.uk/api/mono/products/v1/downloads/scripted?path=grch{grch_version}/cell_lines/v{cosmic_version}/CellLinesProject_GenomeScreensMutant_Tsv_v{cosmic_version}_GRCh{grch_version}.tar&bucket=downloads"