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tkzeng / Pangolin

Pangolin is a deep-learning method for predicting splice site strengths.
GNU General Public License v3.0
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error while running the pangolin script #17

Open sruthisrini opened 6 months ago

sruthisrini commented 6 months ago

Hey,

These are the versions for packages I used: pangolin (1.0.2) pyvcf (0.6.8) pyfaidx (0.8.1.1) gffutils (0.12) biopython (1.83)

I used this command with vcf as input file: pangolin /Pangolin/examples/cosmic_pangolin.vcf /gencode.v43.pc_transcripts.fa /Pangolin/gencode.v38.annotation.db cosmic_pangolin

The error I got:

Using CPU
Traceback (most recent call last):
  File "/Users/sruthisrinivasan/miniconda3/bin/pangolin", line 8, in <module>
    sys.exit(main())
  File "/Users/sruthisrinivasan/miniconda3/lib/python3.10/site-packages/pangolin/pangolin.py", line 244, in main
    variants.infos["Pangolin"] = vcf.parser._Info(
TypeError: Info.__new__() missing 1 required positional argument: 'type_code'

Please help in solving this issue.

Thanks, Sruthi