def __init__(self, vcf_fhand, parents_a, parents_b,
parent_index_threshold=DEF_AB_CODER_THRESHOLD,
offspring=None, window=DEF_AB_CODING_WIN,
smooth_threhsold=None, recomb_threshold=None):
# TODO a min number of genotypes to evaluate anything
self._reader = pyvcfReader(vcf_fhand)
self._offspring = offspring
self.window = window
self.parent_index_threshold = parent_index_threshold
self.log = Counter()
self.indexes = array('f')
samples = self._reader.samples
parents = set(parents_a + parents_b)
missing_parents = parents.difference(samples)
if missing_parents:
msg = 'Some parents are not found in the vcf file: '
msg += ','.join(missing_parents)
raise ValueError(msg)
self.parents_a = parents_a
self.parents_b = parents_b
self.smooth_threhsold = smooth_threhsold
self.recomb_threshold = recomb_threshold
self._recombs = array('B')
self._smoothes = array('f')
def __init__(self,
vcf_fhand,
parents_a,
parents_b,
parent_index_threshold=DEF_AB_CODER_THRESHOLD,
offspring=None,
window=DEF_AB_CODING_WIN,
smooth_threhsold=None,
recomb_threshold=None):
# TODO a min number of genotypes to evaluate anything
self._reader = pyvcfReader(vcf_fhand)
self._offspring = offspring
self.window = window
self.parent_index_threshold = parent_index_threshold
self.log = Counter()
self.indexes = array('f')
samples = self._reader.samples
parents = set(parents_a + parents_b)
missing_parents = parents.difference(samples)
if missing_parents:
msg = 'Some parents are not found in the vcf file: '
msg += ','.join(missing_parents)
raise ValueError(msg)
self.parents_a = parents_a
self.parents_b = parents_b
self.smooth_threhsold = smooth_threhsold
self.recomb_threshold = recomb_threshold
self._recombs = array('B')
self._smoothes = array('f')
def __init__(self, fhand, compressed=None, filename=None,
min_calls_for_pop_stats=DEF_MIN_CALLS_FOR_POP_STATS):
self.fhand = fhand
self.pyvcf_reader = pyvcfReader(fsock=fhand, compressed=compressed,
filename=filename)
self.min_calls_for_pop_stats = min_calls_for_pop_stats
self._snpcaller = None
self._samples = self.pyvcf_reader.samples
self._header_lines = self.pyvcf_reader._header_lines
self._column_headers = self.pyvcf_reader._column_headers