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missing data is ignored with variant files but not .Rtab #157
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I think this is due to the fact that we do not really expect missing values in an .Rtab file, whereas they can be quite common in vcf files. I think we could implement your proposed change to be more consistent. Just out of curiosity, was the .Rtab file you were using coming out of panaroo/roary? If so I was not aware of the fact that it could contain missing values |
Makes sense. No, it was a custom .Rtab file. |
Ok that makes sense. If you would like to open a PR we could merge this change. If you know how to add unit tests that would also be great. If not, I can do it once the change it's merged |
will do |
Missing genotypes in variant files are ignored:
pyseer/pyseer/input.py
Lines 485 to 486 in 2e27979
However, in .Rtab files they are treated as missing data and the fit fails later on:
pyseer/pyseer/input.py
Lines 423 to 424 in 2e27979
Is this intended? For now I have replaced
d[sample] = np.nan
withcontinue
to also get a fit for genes with a few missing entries.The text was updated successfully, but these errors were encountered: