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kr-colab / locator

deep learning prediction of geographic location from individual genome sequences
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Issue: sample data matches, but sample ordering failed! message still appears #16

Closed clararehmann closed 4 years ago

clararehmann commented 4 years ago

Hi,

I'm working with genotypes in .zarr format - sample IDs in the Zarr array have been written directly from the metadata file, and I am reading them into Locator as strings with .astype('str') appended to samples = callset['samples'][:]. Sample IDs match the metadata according to my test script, but when I run Locator, I get the following error message:

sample ordering failed! Check that sample IDs match the VCF.

Reproducing code example

$ python test.py
> no output
$ python locator/scripts/locator.py --zarr zarr/2L.zarr --sample_data ag1000g3_sample.txt --out out --windows --window_size 2000000
> sample ordering failed! Check that sample IDs match the VCF.

issue.zip

Thanks!

andrewkern commented 4 years ago

hey @clararehmann. i found the issue on the locator side. PR #17 closes this out.