I appreciate the example notebooks you provided for parsing the nirvana output json files. I had great success expanding on those notebooks and parsing the toy vcf you all provided.
However, when I attempt to use those same scripts on the files my lab generated, I get a few errors that do not occur with the toy files. First when I parse the header exactly the same as the example notebook, I get the following traceback:
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 5375: ordinal not in range(128)
The other two examples in that notebook, Retrieve all relevant genes and their OMIM gene names and Retrieve variants under a gnomAD allele frequency threshold, both generate empty data frames when I attempt to use them on my data. No tracebacks, just empty data frames. Again, these examples work exactly as one would expect when tested on the ceph_trio_test.json.gz toy file provided.
Has the json output format changed in a significant way since those examples were generated, or should I expect them to be functional on our Nirvana outputs as well as the test files?
The version my lab uses is Nirvana 3.21.0-0-gd2a0e953
Thanks for any help you can offer!
Hi there!
I appreciate the example notebooks you provided for parsing the nirvana output json files. I had great success expanding on those notebooks and parsing the toy vcf you all provided.
However, when I attempt to use those same scripts on the files my lab generated, I get a few errors that do not occur with the toy files. First when I parse the header exactly the same as the example notebook, I get the following traceback:
The other two examples in that notebook, Retrieve all relevant genes and their OMIM gene names and Retrieve variants under a gnomAD allele frequency threshold, both generate empty data frames when I attempt to use them on my data. No tracebacks, just empty data frames. Again, these examples work exactly as one would expect when tested on the
ceph_trio_test.json.gztoy file provided.Has the json output format changed in a significant way since those examples were generated, or should I expect them to be functional on our Nirvana outputs as well as the test files?
The version my lab uses is
Nirvana 3.21.0-0-gd2a0e953Thanks for any help you can offer!