missing data is ignored with variant files but not .Rtab

[julibeg]

Missing genotypes in variant files are ignored:

pyseer/pyseer/input.py

Lines 485 to 486 in 2e27979

	elif sample in d and np.isnan(d[sample]) and str(haplotype) != '.':
	del d[sample]

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

	elif present == ".":
	d[sample] = np.nan

Is this intended? For now I have replaced d[sample] = np.nan with continue to also get a fit for genes with a few missing entries.

[mgalardini]

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

[julibeg]

Makes sense.

No, it was a custom .Rtab file.

[mgalardini]

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

[julibeg]

will do