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CSuperlei / DeepSV

Calling deletions using deep convolutional neural
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Failed to run the script(s) #3

Open arnikz opened 4 years ago

arnikz commented 4 years ago

Hi,

I've tried to run the script(s) as described in the README.md but got stuck on the way. Please see my suggestions in this PR. The command-line interface does not include e.g. -h|--help (nor input VCF file). 

Traceback (most recent call last):
  File "Deletion_Image_Source/Generate_Deletion_Image.py", line 78, in <module>
    main()
  File "Deletion_Image_Source/Generate_Deletion_Image.py", line 50, in main
    vcf_file = file.get_vcf_file(vcf_path,'deletion')   
  File "/home/arnikz/Downloads/DeepSV/Deletion_Image_Source/FILE_CLASS.py", line 3, in get_vcf_file
    deletion_pos = open(vcf_path,'r')
FileNotFoundError: [Errno 2] No such file or directory: 'your file path'

Could you add a working example including a small dataset? Thank you.

FEIFEIEIAr commented 2 years ago

For your problem, you should change 'your file path' to your own path, like '/home/.../your_vcf.vcf', in line 78 of Generate_Deletion_Image.py. However, I read some codes of DeepSV, I found a lot of mistakes, which means that you should change plenty of codes then you can really run it.

chycheng2015 commented 1 year ago

I also found that these scripts contain many mistakes, and are not consistent with what are described in the paper published on BMC bioinformatics