Started riboswitch generation code. Completed N randomization and on switch validation for ribozymes.
Added function to interface with RNAstructure (RNA_structure) ribozyme_forming now works for any number of continuous Ns in the 5' transmitter. Writes out sequences as soon as they are found to text file found.txt and the whole catalog to catalog.csv at the end.
Made bug fixes to RNA_structure in Riboswitch_generation and removed running all functions. Created Riboswitch_cleanup with remove_matching, top_X, unwanted_structures, ribo_on, ribo_off, bond_breaker, csv_write. Created Ribozyme_Runner which is all is needed to edit for finding new sequences.
Fixed repeating sequences in Riboswitch_generation. Added the keeping of .fasta, .ct, and dotbracket files to on_catalog and off_catalog.
Added ReadMe file containing instructions for ribozyme finding
Added sequence list to fasta and PIM to top matches ability to Sequence_Analysis. Still listed under seq_cleanup function. fasta to PIM must be done manually though Clustal Omega webserver.
Split out ribozyme_length_mode, fasta_write_mode, and pim_reader into their own functions.