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filter out viruses from NCBI Taxonomy 'unclassified' #126

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realmarcin opened this issue Feb 26, 2024 · 1 comment
Open

filter out viruses from NCBI Taxonomy 'unclassified' #126

realmarcin opened this issue Feb 26, 2024 · 1 comment

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@realmarcin
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These viruses are found in the ncbitaxon_removed_subset.json:

"val" : "Cotton leaf curl Rajasthan virus betasatellite defective interfering DNA"
"lbl" : "Cotton leaf curl Rajasthan virus defective interfering DNA",
"lbl" : "Cotton leaf curl virus betasatellite defective interfering DNA",
"lbl" : "Hygrophorus parvirussula",
"lbl" : "unidentified Cotton leaf curl Rajasthan virus-associated DNA",

@realmarcin
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@bsantan let's think about how to add this to the transform code. I believe filtering on no 'virus' or 'phage' in the reference proteome names will work. We can say we assume that no multicellular organism is 'unclassified' -- though this may not be entirely true. The first pass/test transform could just exclude anything from 'unclassified'.

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