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gagneurlab / MMSplice_MTSplice

Tissue-specific variant effect predictions on splicing
MIT License
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VEP plugin writes Tensorflow startup messages to stdout #8

Closed aerval closed 5 years ago

aerval commented 5 years ago

I am running the VEP MMSplice plugin using --output_file STDOUT to pipe the results. However the tensorflow startup messages gets also forwarded and ends up in the pipe. It can be removed with | grep -v tensorflow but thats obviously not ideal.

MuhammedHasan commented 5 years ago

Thanks for the issue. You are right about the issue. In our code, we filter stdout and print only related content. But Tensorflow somehow bypasses this filter. It doesn't show up in stdout (even in os level) but show up in the terminal :thinking:.

Similary, you can run following terminal comment. I also create PR to update the documentation. 

cat tests/data/test.vcf | sudo docker run -i mmsplice vep --plugin MMSplice --format vcf --assembly GRCh37 --database --port 3337 --vcf -o STDOUT | tee log_variant_effect_output.txt
sed -n '/##fileformat=VCFv4.0/,$p' log_variant_effect_output.txt > variant_effect_output.vcf