Funcotator - COSMIC data for overlapping mutations should list protein changes

[jonn-smith]

Currently the COSMIC_overlapping_mutations field produces only a count, rather than a count for each protein change.

It should look like this:

p.L858R(1489)| p.L858Q(1)| p.L858K(1)

[jonn-smith]

Need to investigate if COSMIC has transcript information to make these annotations correct.

At a minimum can just duplicate Oncotator functionality here.

[jonn-smith]

Before anything else, check to see if this is really a beta blocker.

Check with @LeeTL1220 to see what Oncotator does for this case.

[jonn-smith]

From Lee:

he COSMIC datasource in oncotator simply finds all overlapping records and counts the protein change ("Mutation AA") values. Like a histogram of all overlapping records. (edited)

mutation_AAs = collections.Counter([entry['Mutation AA'] for entry in overlapping_cosmic_entries])

[jonn-smith]

Looks like COSMIC should contain all the needed info to create this annotation properly. Will adjust LOE for this issue (7->2)

[jonn-smith]

@LeeTL1220 Should the default funcotation here be an empty string, or "0"? Currently it's the latter, but with this update it seems that with this change we should switch to empty string.