Comments (5)
chrishendra93
commented on July 29, 2024
1
Thank you for the response! After checking your eventalign.txt closely, it seems that your nanopolish run does not produce the column start_idx and end_idx that is required by m6anet to preprocess the file. You need to include --signal-index option in your nanopolish eventalign command, let me know if it is working for you!
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chrishendra93
commented on July 29, 2024
Hi @FraPria, thanks for raising this issue. Can I check whether data.json contains all NaN, or if those are the only entries with NaN? Can you show me the output of data.index as well? If data.index output is fine, then do you think you can give me a minimal reproducible example that results in this error? Perhaps you can extract eventalign outputs only from those positions with NaN entries
I don't expect m6anet-run_inference to run successfully given those outputs but thanks for raising this, in the future I will include some checks to make sure that it will not run if there is a problem with data.json
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FraPria
commented on July 29, 2024
Hi @chrishendra93, thanks for your answer!
the output of data.index is like this:
transcript_id,transcript_position,start,end
68ebd370-cef0-4b97-bd1b-825d623446e2_chr1:18000,2170,0,113
68ebd370-cef0-4b97-bd1b-825d623446e2_chr1:18000,3061,113,226
68ebd370-cef0-4b97-bd1b-825d623446e2_chr1:18000,3153,226,377
68ebd370-cef0-4b97-bd1b-825d623446e2_chr1:18000,3159,377,528
68ebd370-cef0-4b97-bd1b-825d623446e2_chr1:18000,3565,528,641
c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463,101,641,986
c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463,156,986,1293
c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463,194,1293,1600
c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463,228,1600,2021
Here I attach a subset of the eventalign output
eventalign.txt
Running the command:
m6anet-dataprep --eventalign eventalign.txt --out_dir .
I get this output:
{"68ebd370-cef0-4b97-bd1b-825d623446e2_chr1:18000":{"2170":{"GAGACAT":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
{"68ebd370-cef0-4b97-bd1b-825d623446e2_chr1:18000":{"3153":{"GTGACCC":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
{"68ebd370-cef0-4b97-bd1b-825d623446e2_chr1:18000":{"3159":{"CTGACTT":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
{"c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463":{"101":{"AAGACAC":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
{"c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463":{"194":{"CTGACCA":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
{"c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463":{"228":{"AAAACAA":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
{"c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463":{"303":{"ATGACAG":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
{"c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463":{"398":{"GTAACAA":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
{"c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463":{"418":{"TAAACTG":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
{"c6e29c47-9e37-427a-81d5-70e87a061505_ENSG00000228463":{"436":{"CTAACTC":[[NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN]]}}}
It outputs also a warning:
site-packages/m6anet-0.1.1-py3.7.egg/m6anet/scripts/dataprep.py:143: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead
See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
Thank you
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FraPria
commented on July 29, 2024
That was the problem, now it gives the expected output, thanks a lot!
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chrishendra93
commented on July 29, 2024
Hi @FraPria, glad that you can run the model successfully. I will update the documentation with this instruction just in case so that people know what commands to supply to Nanopolish in order to run the model successfully. I will now close this issue, let us know if you have any more problems running the model!
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