writeVCF not implemented. I wrote some implementation

[beskns]

columns = [
'gene_name',
'transcript_id',
'exons',
'ref_exon',
'alt_exon',
'ref_donor',
'alt_donor',
'ref_acceptor',
'alt_acceptor',
'ref_acceptorIntron',
'alt_acceptorIntron',
'ref_donorIntron',
'alt_donorIntron',
'delta_logit_psi',
'pathogenicity',
'efficiency'
]

def writeVCF(vcf_in, vcf_out, predictions):
from cyvcf2 import VCF, Writer
vcf = VCF(vcf_in)
vcf.add_info_to_header({
'ID': 'mmsplice',
'Description': 'MMSplice splice variant effect. Format:' + '|'.join(columns),
'Type': 'Character',
'Number': '.'
})
w = Writer(vcf_out, vcf)

for var in vcf:
    ID = f"{var.CHROM}:{var.POS}:{var.REF}:{var.ALT}"
    pred = predictions[predictions.ID == ID]
    if pred is not None:
        pred_4_var = [
            '|'.join([row[k] for k in columns[:3]]) + '|' +
            '|'.join([format(row[k], ".3f") for k in columns[3:]])
            for ind, row in pred.iterrows()
        ]
        var.INFO['mmsplice'] = '&'.join(pred_4_var)
    w.write_record(var)

[MuhammedHasan]

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.

[beskns]

It is only stub. Not working! 25.09.2019, 19:48, "Muhammed Hasan" <notifications@github.com>:Thanks for your contribution but writeVCF is already implemented. https://github.com/gagneurlab/MMSplice/blob/7f4aeb8bfa6cd460bccc5db593c066d1691bf1f6/mmsplice/mmsplice.py#L193 —You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or mute the thread. -- С уважением,Н.С. Бескоровайный

[s6juncheng]

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.

[tstohn]

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

[s6juncheng]

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.

[tstohn]

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