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# Copyright 2000 by Iddo Friedberg idoerg@cc.huji.ac.il
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
r"""A class to handle frequency tables or letter count files.
Example files for a DNA alphabet:
A count file (whitespace separated)::
A 50
C 37
G 23
T 58
The same info as a frequency file::
A 0.2976
C 0.2202
G 0.1369
T 0.3452
Functions:
:read_count(f): read a count file from stream f. Then convert to
frequencies.
:read_freq(f): read a frequency data file from stream f. Of course, we then
don't have the counts, but it is usually the letter frequencies
which are interesting.
Methods:
(all internal)
Attributes:
:alphabet: The letters you are using as indices into the table.
:data: Frequency dictionary.
:count: Count dictionary. Empty if no counts are provided.
Example of use:
>>> import io
>>> from Bio.SubsMat import FreqTable
>>> f_count = io.StringIO(u"A 50\nC 37\nG 23\nT 58")
>>> ftab = FreqTable.read_count(f_count)
>>> for nb in sorted(ftab):
... print("%s %0.4f" %(nb, ftab[nb]))
...
A 0.2976
C 0.2202
G 0.1369
T 0.3452
"""
COUNT = 1
FREQ = 2
class FreqTable(dict):
"""Define class to handle frequency tables or letter count files."""
def _freq_from_count(self):
"""Calculate frequency from count values (PRIVATE)."""
total = float(sum(self.count.values()))
for i, v in self.count.items():
self[i] = v / total
def _alphabet_from_input(self):
"""Order the alphabet (PRIVATE)."""
s = ""
for i in sorted(self):
s += i
return s
def __init__(self, in_dict, dict_type, alphabet=None):
"""Initialize the class."""
self.alphabet = alphabet
if dict_type == COUNT:
self.count = in_dict
self._freq_from_count()
elif dict_type == FREQ:
self.count = {}
self.update(in_dict)
else:
raise ValueError("bad dict_type")
if not alphabet:
self.alphabet = self._alphabet_from_input()
def read_count(f):
"""Read a count file f and load values to the Frequency Table."""
count = {}
for line in f:
key, value = line.strip().split()
count[key] = int(value)
return FreqTable(count, COUNT)
def read_freq(f):
"""Read a frequency data file f and load values to the Frequency Table."""
freq_dict = {}
for line in f:
key, value = line.strip().split()
freq_dict[key] = float(value)
return FreqTable(freq_dict, FREQ)
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