Add additional functionality for alignment compare script!

[emmahodcroft]

Building on the initial great script to compare alignments, I've added some additional functionality to make it more flexible and generalizable!

@kstrotjohann you should check it still works on your data appropriately before it gets merged!

In the long-term we may want to break scripts like this into another repo so they can be easily found and re-used 😁

Changes:

• added an argument to reduce printing messages unless --verbose is specified
• Rectified a FutureWarning
• Change font to matplotlib default so it should work on any system (turns out I don't have Arial! 🤔 )
• Generalize plotting so it works with any number of alignments being compared (colours, columns, names)
• Added an argument (--cds-coords) so one can give the start-end of the coding region and just compare these (allows one to not have to trim sequences to the coding region beforehand!)

Tests run:

• I ran on two alignments (EV-D68) after each change to ensure code runs and answers are reasonable sensible
• However I did not check to see if the counts etc are valid (ex: counting stop muts myself and comparing to the code) as in theory none of the changes I made should impact this -- hoping that Keno can check against his original runs 😁

[emmahodcroft]

Added one more change - changed the sum-of-pairs plot to be a scatterplot with variable-Y-axis rather than a bar chart. The numbers are very large and can be sometimes different, sometimes very similar, this helps to allow that adjustment a bit better.

Not exactly the same plot, but an example of before and after.
Before:

After: