Issue with Zero Division Error

[tegar9000]

When I run ClassifyCNV.py, I get
"File "/gpfs52/data/ruderferlab/sandbox/tucker/Scripts/ClassifyCNV/ClassifyCNV.py", line 737, in analyze_pop_freqs
overlap_perc = int(fields[9]) * 100 / (int(fields[2]) - int(fields[1]))
ZeroDivisionError: division by zero"
I inputted a bedfile and I am not sure how to interpret this error in the context of the code.

Your help would be seriously appreciated. Thanks!

[tgurbich]

Hi tegar9000,

Does your input bed file have CNVs where the start and end positions are the same (meaning their length is 0)? Unfortunately, ClassifyCNV cannot analyze such CNVs since their sequence is not available. I would recommend prefiltering your input file to remove 0-length CNVs and running ClassifyCNV again. If that wouldn't work and you need them analyzed, I'd recommend looking for a different tool.

Hope this helps. Please let me know if you have any further questions.

Tanya

[tegar9000]

Yep that works! Thanks again

One other thing: regarding the scoresheet.txt file, is there a format I can convert the file into or a software I can use to analyze my results? Was wondering how since I am much of an ameteur programmer lmao

[tgurbich]

Great! In terms of analyzing the results, it depends on what you want to get out of it. It might be enough to just look at the final pathogenicity score. It might be easiest to use Excel to navigate the results but again, depends on what you'd like to do. I am not aware of any other software for this, sorry!