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jeffhussmann / knock-knock

toolkit for analyzing genome editing experiments
GNU General Public License v3.0
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pegRNAs are not defined in example data #4

Closed ShanSabri closed 2 years ago

ShanSabri commented 2 years ago

Hi @jeffhussmann, please see below on error produced using example data: 

$ knock-knock build-indices $PROJECT_DIR $ORGANISM --num-threads $NUM_THREADS
Downloading hg38...
Uncompressing...
Building indices for hg38
Indexing fastas...
Building STAR index...
Building minimap2 index...

$ knock-knock build-targets $PROJECT_DIR
Traceback (most recent call last):
  File "/home/ubuntu/.Anaconda3/bin/knock-knock", line 236, in <module>
    args.func(args)
  File "/home/ubuntu/.Anaconda3/bin/knock-knock", line 122, in build_targets
    build_targets.build_target_infos_from_csv(args.project_directory,
  File "/home/ubuntu/.Anaconda3/lib/python3.8/site-packages/knock_knock/build_targets.py", line 1142, in build_target_infos_from_csv
    for pegRNA_name, pegRNA_components in info['pegRNAs']:
TypeError: 'NoneType' object is not iterable

Any insight on how best to proceed?

ShanSabri commented 2 years ago

Ended up downgrading to knock-knock==0.3.6

jeffhussmann commented 2 years ago

Hi @ShanSabri - this particular bug should be fixed by dbaa5a33865c47b9d427a74ba6068eb1527e7fc9, but if you are not using the (currently undocumented) prime editing support, then downgrading was the correct approach.