Function to classify uORFs mutations

[Ale-pinto-alba]

• Create a function to classify uORFs mutations. I commented this in the visualization branch, but there I classified them in a very rudimentary way, so I decided to make this function to ease it.

[Ale-pinto-alba]

• I created a class instead of a single function with several parameters. Then I used some logic to check which type of mutation is the variant causing.
• To check if the variant affects the start codon I kept the same logic, comparing the number of uORFs between the canonical and the variant.
• To check if the variant affects the stop codon, I created two methods:

stop codon loss: if the variant uORF is longer than the canonical one, it is overlapping and the variant position is in the range of the three nucleotides before the end of the uORF, therefore, I can assume that this variant is provoking the loss of this stop codon.

stop codon gain: if the variant uORF is shorter and not overlapping, I think it can be assumed that a stop codon appeared.

• To check insertions, deletions and so on, if it is not one of the previous mutations, I consider it can be assumed that a longer variant uORF is an insertion, a shorter a deletion and if each uORF has the same length, it should be a SNV or a MNV.

• Finally, I put this methods as private ones, because I think they should be done in order, then, I created the perform_mutation_analysis to make sure of this.

• Create tests for each type of mutation.

*** I am not 100x100 sure if the logic behind this class is completely correct.
*** Probably is too much to ask in a __init__, but I believe this interpretation is better than the previous one, so we can discuss it tomorrow :)