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def frequency_median(frequencies):
"""
Given a dictionary of frequencies, return the median.
If the total no. of values is odd, the left of both
middle values is returned.
"""
m = 0 # partial sum
middle = (1 + sum(frequencies.values())) // 2
for length in sorted(frequencies):
m += frequencies[length]
if m >= middle:
return length
# never reached
assert False
def frequency_n50(lengths, genome_size=None):
"""
Return N50 or NG50 value given a Counter of lengths.
If the genome_size is not given, it is set to the total length. The resulting
value is the N50. If it is given, the resulting value is the NG50.
If genome_size is greater than two times the number of sequences, None is returned.
"""
if genome_size is None:
genome_size = sum(length * count for length, count in lengths.items())
running_total = 0
for length in sorted(lengths, reverse=True):
running_total += length * lengths[length]
if running_total >= genome_size * 0.5:
return length
return None
def n50(lengths, genome_size=None):
"""
Return N50 or NG50 value given a list of lengths.
If the genome_size is not given, it is set to sum(lengths). The resulting
value is the N50. If it is given, the resulting value is the NG50.
If genome_size is greater than 2 * sum(lengths), None is returned.
"""
if genome_size is None:
genome_size = sum(lengths)
lengths = sorted(lengths, reverse=True)
running_total = 0
for length in lengths:
running_total += length
if running_total >= genome_size * 0.5:
return length
return None
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