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mgalardini / pyseer

SEER, reimplemented in python 🐍🔮
http://pyseer.readthedocs.io
Apache License 2.0
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--max-missing in pyseer is not working. #120

Closed neginmb closed 4 years ago

johnlees commented 4 years ago

Can you please provide more details? The version you are using, the command being run, the file that produces this behaviour, what is expected, and what is seen?

If possible, a small file (for example a single variant with missing data) that reproduces your problem would help us.

neginmb commented 4 years ago

I am using pyseer v1.3.0, this is my command: pyseer --phenotypes pheno-continuous.tsv --vcf normalized_test.vcf \ --no-distances \ --max-missing 0.01 \

test-output.txt

My file has only one variant with high missingness (around 18%), but it didn't get filtered by this command.

Dear @johnlees , how can I send my example file to you?

mgalardini commented 4 years ago

Hi, see here for a guide on how to attach files to a github issue

neginmb commented 4 years ago

Hi, this is my file: normalized_test.zip

mgalardini commented 4 years ago

Hi, I think the issue has now been fixed. Could you try to download the latest master and try it yourself? Thanks

neginmb commented 4 years ago

I couldn't run the latest Master. What if I upgrade my pyseer directly with pip command? then the upgraded one has the bug fixed?

mgalardini commented 4 years ago

You can download the latest master here; unzip it, cd into it and then run your original command like this: python3 pyseer-runner.py [ARGS].