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pinellolab / CRISPRme

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CRISPRme ERROR: CFD radar chart report failed #39

Closed anurendra closed 1 year ago

anurendra commented 1 year ago

Gives me above error for few guides(not all). In particular L121 in radar_chart_dict_generator.py- 'if guide[count] == 'N':', error is IndexError: string index out of range.

samuelecancellieri commented 1 year ago

Hi @anurendra can you attach the full log_error and guide file with all the guides you are using? I think the problem may be different lengths in the guides, since this is not expected.

Thanks a lot.

anurendra commented 1 year ago

Here is a guide for which it occurs- GGGGCCACTAGGGACAGGAT. Attaching log report log_error.txt

samuelecancellieri commented 1 year ago

hello @anurendra

the problem i see in the guide you attached, is the absence of 'N's. a guide should look like this, AAAAAAAANNN or NNNNAAAAAAAAA depending if the PAM sequence is upstream or downstream.

if you downloaded the test dataset, you have a file called sg1617.txt and this is how a guide should be written. the software expected the presence of Ns in the guide sequence to identify the position of the PAM and the length. add the Ns nucleotide in place of the PAM sequence attached to the guide, and this should solve the problem.

let me know.

thanks,