1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
|
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# Copyright Iddo Friedberg idoerg@cc.huji.ac.il
"""A class to handle frequency tables
Methods to read a letter frequency or a letter count file:
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 frquencies which are
interesting.
Methods:
(all internal)
Attributes:
alphabet: The IUPAC alphabet set (or any other) whose letters you are
using. Common sets are: IUPAC.protein (20-letter protein),
IUPAC.unambiguous_dna (4-letter DNA). See Bio/alphabet for more.
data: frequency dictionary.
count: count dictionary. Empty if no counts are provided.
Example of use:
>>> from SubsMat import FreqTable
>>> ftab = FreqTable.FreqTable(my_frequency_dictionary,FreqTable.FREQ)
>>> ftab = FreqTable.FreqTable(my_count_dictionary,FreqTable.COUNT)
>>> ftab = FreqTable.read_count(open('myDNACountFile'))
"""
from Bio import Alphabet
COUNT = 1
FREQ = 2
class FreqTable(dict):
def _freq_from_count(self):
total = float(sum(self.count.values()))
for i, v in self.count.items():
self[i] = v / total
def _alphabet_from_input(self):
s = ''
for i in sorted(self):
s += i
return s
def __init__(self, in_dict, dict_type, alphabet=None):
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 = Alphabet.Alphabet()
self.alphabet.letters = self._alphabet_from_input()
def read_count(f):
count = {}
for line in f:
key, value = line.strip().split()
count[key] = int(value)
freq_table = FreqTable(count, COUNT)
return freq_table
def read_freq(f):
freq_dict = {}
for line in f:
key, value = line.strip().split()
freq_dict[key] = float(value)
return FreqTable(freq_dict, FREQ)
|
