Refactored + full functionality

Refactored the project into 3 scripts: main.py (script to run project), fragmentation_v2.py (to be renamed onced finalised), and utils.py (auxillary functions for command-line arguments). Edited code to now (only) accept FASTA and CSV files for the cDNA sequences and seq counts, respectively, and pre-process these for use by the fragmentation function.