When you use your own index with -x and -d, the "transcript_to_gene_info.pickle" file is never loaded and the code crashed after trying to write the "info_dict" variable that is never created.
Easy fix, load the file after "transcript_to_CDS.pickle" is loaded at line 465 in init.py.
Add something like:
info_path = os.path.join(args.dicts, "transcript_to_gene_info.pickle")
if os.path.isfile(info_path):
with open(info_path, "rb") as info_stream:
info_dict = pickle.load(info_stream)
else:
raise RuntimeError(
"".join(
[
"Cannot find ",
info_path,
"; have you indexed your GTF with neoepiscope index?",
]
)
)
When you use your own index with
-x
and-d
, the "transcript_to_gene_info.pickle" file is never loaded and the code crashed after trying to write the "info_dict" variable that is never created.Easy fix, load the file after "transcript_to_CDS.pickle" is loaded at line 465 in init.py. Add something like: