refactor: update CLI

• Refactored cli.py, where the fasta dict couldn't be sliced
• Updated cli.py so the tool can now be installed with pip install . and works from the command line
• Refactored some of the code to fix CI pipeline failing
• Updated README

term_frag_sel/fragmentation.py

@@ -24,7 +24,7 @@ def fragmentation(fasta: dict, seq_counts: pd.DataFrame,
 
     term_frags = []
     for seq_id, seq in fasta.items():
-        counts = seq_counts[seq_counts["seqID"] == str(seq_id)]["count"]
+        counts = seq_counts[seq_counts["seqID"] == seq_id]["count"]
         for _ in range(counts.iloc[0]):
             cuts = []
             seq_len = len(seq)