Moved TFBS num_sites attribute
Style and commenting
Rearranged command line processing
Set up command line processing and all() function
Style and commenting
Chromosome-specific running of all TF pairs
Removed print statements in generate_data()
Removed print statements in freq_study()
Removed print statements in main()
Fixed print statement syntax in main()
Rearranged global statements
Fixed print statement syntax in main()
Rearranged print statements in main()
Rearranged print statements in main()
Rearranged comments in main()
Flush stdout buffer at beginning of main()
Temporarily removing CHR from --all option
Rearranged flush stdout buffer
Separate run() function that will eventually be called by all()
Testing extraction of names and codes in all()