All the HMM helper functions are in HMM.py and HMM_helper.py. These are mostly specific to the HMMs, but occasionally feature elements such as punctuation or list generation. Syllable and Rhyme implementations in Final_HMM.
The character based RNN described in section 4 of the report is in character_RNN. The improved RNN that is word based (described in section 6) is in word_RNN.