def test_order():
o1 = order([132, 99, 22], ordering=[99, 22, 44, 132])
o2 = order([{'thing': 'bathrobe'}, {'thing': 'toga'}],
['toga', 'bathrobe'], key='thing')
o3 = order([-2, 2, 4, 1, 4],
[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16], key=lambda x: x * x)
asserts.eq_(o1, [99, 22, 132])
asserts.eq_(o2, [{'thing': 'toga'}, {'thing': 'bathrobe'}])
asserts.eq_(o3, [1, -2, 2, 4, 4])
def genotypes_to_records(genotypes, reader, extant_columns):
"""Return a list of vcf.model._Record, converted from a list of genotype
relations, taken from the database.
This is used to write to a .vcf file with vcf.parser.Writer.
Args:
genotypes: a list of genotype relations from the database.
reader: a template vcf.Reader.
extant_columns: a list of columns which have values for these genotypes.
"""
info_fields, format_fields = _fields_from_columns(extant_columns)
CallData = vcf.model.make_calldata_tuple(format_fields)
grouped_genotypes = itertools.groupby(genotypes, _call_key)
sample_ordering = reader.samples
records = []
for _, gts in grouped_genotypes:
samples = []
gts = list(gts)
gts = order(gts, sample_ordering, 'sample_name')
for gt in gts:
data = CallData(*[vcf_format(gt['sample:' + d]) for d in format_fields])
call = vcf.model._Call(None, gt['sample_name'], data)
samples.append(call)
record = _make_record_from_gt(gts[0], info_fields, format_fields, samples)
records.append(record)
return records
