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MuhammedHasan avatar MuhammedHasan commented on July 27, 2024

Thanks for your contribution but writeVCF is already implemented.

https://github.com/gagneurlab/MMSplice/blob/7f4aeb8bfa6cd460bccc5db593c066d1691bf1f6/mmsplice/mmsplice.py#L193

If you think this implementation is lacking some of the features, please report them. We can improve the implementation.

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beskns avatar beskns commented on July 27, 2024

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s6juncheng avatar s6juncheng commented on July 27, 2024

thanks @beskns. @MuhammedHasan maybe we put it in the utils.py and import to the first level in the init.py file for the next release.

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tstohn avatar tstohn commented on July 27, 2024

Are there any news regarding the WriteVcf functionality.
We would also be thrilled to use it in the MedGen in Tübingen.
Thanks,
Tim

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s6juncheng avatar s6juncheng commented on July 27, 2024

This function is now implemented in mmsplice.utils.writeVCF

MMSplice_MTSplice/mmsplice/utils.py

Line 353 in dd91265

def writeVCF(vcf_in, vcf_out, predictions):

New version is on pypi and can be installed with pip.

Thanks @beskns for sharing your implementation. I did some modifications based on that.

After writing the predictions as vcf file, you can read the output file into a pandas DataFrame with mmsplice.utils.read_vep

MMSplice_MTSplice/mmsplice/utils.py

Line 164 in dd91265

def read_vep(vep_result_path,

Hopefully, this works for your use case @tstohn.

I close the issue for now, please feel free to reopen if there is further question or request.

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tstohn avatar tstohn commented on July 27, 2024

Hey Jun,
Thanks a lot. That works for me.
Only thing I was wondering was, that i was getting a segfault when writing a variant list, for which some variants have
no mmsplice prediction.
I noticed it to be due to 'pred' in line 384 in utils.py beeing an empty DataFrame, which holds no values, which are then accessed in line 387.
In case you can not reproduce this let me know and I ll have a deeper look into it on my machine.
Thanks again & Cheers,
Tim

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