Python checkRare Examples

Example #1

File: countExacTotalVars.py Project: samesense/target_exac_setup

def getCounts(ref, countLs, key, altLs, oneKPopInfo, effField):
    """Rm indels, non-rare 1kg, and non-func vars."""
    finalCountLs = []
    effectVars = parseEffectVars(effField)
    for count, alt in zip(countLs, altLs):
        isRare = filterExac1kg.checkRare(oneKPopInfo, (alt,), ref, key)
        if isRare and len(alt) == 1 and len(ref) == 1 and alt in effectVars:
            finalCountLs.append(count)
    return finalCountLs

Example #2

File: countExacGeneVars.py Project: samesense/target_exac_setup

def getCounts(ref, countLs, key, altLs, oneKPopInfo, effField, gene, inGoodPos):
    """Rm indels, non-rare 1kg, and non-func vars.
       Indles are filtered by kaviar and cg.
    """
    finalCountLs = []
    effectVars = parseEffectVars(effField, gene)
    for count, alt in zip(countLs, altLs):
        if inGoodPos:
            isRare = filterExac1kg.checkRare(oneKPopInfo, (alt,), ref, key)
            if isRare and alt in effectVars:
                finalCountLs.append(count)
    return finalCountLs