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mskcc / pluto-cwl

CWL workflows for helix filter scripts
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Need to normalize the NA values between concatenated tables #12

Closed stevekm closed 4 years ago

stevekm commented 4 years ago

The Argos .maf files have '' empty string filling in missing values in the .maf files, but the Facets Suite annotated maf files have NA strings instead. When you concatenate you get a mix of both. Need to change them both to the same thing.

Considering updating concat-tables.py script to include a flag such as --normalize-NA-string="" that will let you pass in an old bad NA string to convert to the new one.

stevekm commented 4 years ago

looks like this accidentally gets resolved here in concat-tables.py;

def update_dict(d, keys, default_val):
    for key in keys:
        if not d.get(key, None):
            d[key] = default_val
    return(d)

if the value is '' then it gets set to the NA value anyway