Package Bio :: Package SubsMat :: Module FreqTable
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Module FreqTable

source code

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

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.
(all internal)
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'))
Classes [hide private]
Functions [hide private]
read_count(f) source code
read_freq(f) source code
Variables [hide private]
  COUNT = 1
  FREQ = 2
  __package__ = 'Bio.SubsMat'