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 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'))