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JonJala / mama

MIT License
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SNP ANCES file #30

Closed llandsmeer closed 1 year ago

llandsmeer commented 1 year ago

After stumbling through the different file formats (I do think the documentation could be improved a bit - like at least showing an example of some command invocations and the contents of ances_path; not everybody knows what IID means from the top of their head. or the hidden requirement that the bed file can't contain more ancestries than listed in the ances_path file), I'm now at this error:

    raise IOError('Please specify filepath to snp_ances, a text file with SNP ID and indicator columns for each ancestry group. Note that the header row is required.')
OSError: Please specify filepath to snp_ances, a text file with SNP ID and indicator columns for each ancestry group. Note that the header row is required.

I can't find a reference to this snp_ances file in the preprint or the rest of the documentation. How do I obtain this and why is it needed? I'm using 1kGp3v5 as reference, so if you have one ready for that it would be great

Kind regards, Lennart

llandsmeer commented 1 year ago

We solved this by creating an snp_ances file with all snps and the indicator set to 1 for both ancestries - is this this valid?