gemini-inheritance-api.py

from gemini.gim import AutoDom, AutoRec, DeNovo, MendelViolations, CompoundHet

# turn a dictionary into something that can be accessed by attribute.
class Args(object):
    """
    >>> args = Args(db='some.db')
    >>> args.db
    'some.db'
    """
    _opts = ("columns", "db", "filter", "min_kindreds", "families",
                 "pattern_only", "max_priority", # only for compound_het
                 "allow_unaffected", "min_gq", "lenient", "min_sample_depth")
    def __init__(self, **kwargs):
        if not "min_gq" in kwargs: kwargs['min_gq'] = 0
        if not "lenient" in kwargs: kwargs['lenient'] = False
        for k in ("families", "filter"):
            if not k in kwargs: kwargs[k] = None
        if not "gt_phred_ll" in kwargs: kwargs['gt_phred_ll'] = None
        if not "min_sample_depth" in kwargs: kwargs['min_sample_depth'] = 0

        for k in ("min_kindreds", "max_priority"):
            if not k in kwargs: kwargs[k] = 1
        for k in ("pattern_only", "allow_unaffected"):
            if not k in kwargs: kwargs[k] = False
        self.__dict__.update(**kwargs)


model = AutoDom(Args(db="../test/test.auto_dom.db",
                     columns="chrom,start,end,impact_severity,impact,gene,transcript,max_aaf_all",
                     filter="max_aaf_all < 0.1"))

for i, row in enumerate(model.report_candidates()):
    # row is an OrderedDict
    if i == 0:
        print "\t".join(row.keys())
    print "\t".join(map(str, row.values()))


model = CompoundHet(Args(db="../test/test.comp_het.db",
                     columns="chrom,start,end,impact_severity,impact,gene,transcript,max_aaf_all",
                     gt_phred_ll=100,
                     max_priority=3,
                     allow_unaffected=True))

print

for i, row in enumerate(model.report_candidates()):
    # row is an OrderedDict
    if i == 0:
        print "\t".join(row.keys())
    print "\t".join(map(str, row.values()))


if __name__ == "__main__":
    import doctest
    import sys
    doctest.testmod()