Open manulera opened 1 year ago
hi @kimrutherford, I have made the allele name optional in the API as we discussed yesterday.
I have made the allele name optional in the API as we discussed yesterday.
Thanks. I've changed Canto so that the "Check" button works even if the allele name is blank.
I'm still working on removing the Check button.
By the way, the allele types that can be checked are those that contain either "nucleotide" or "amino" in them.
Is this ticket still required?
Yep, I haven't implement this yet.
I'll work on this after finishing:
Related to #2688
There are three API entry points that can be used to suggest fixes for errors
This works both for allele descriptions and protein modification coordinates, but they have to be comma-separated, so the request should contain the syntax-corrected descriptions. E.g.
V123A, P124A
will not work, it has to beV123A,P124A
./old_coords_fix
Checks whether the coordinates provided match an old gene structure, and if so returns updated coordinates in the
values
field. It also returns a revision where the old coordinates were removed, as well as the coordinates themselves.Example request:
Example response (a list of possible solutions that is empty if no solution exists):
/histone_fix
If the systematic_id corresponds to a histone, check if increasing all indexes by 1 fixes the problem. This is because in histones often the first methionine is not counted.
Example request:
Example response (a list of possible solutions that is empty if no solution exists):
/multi_shift_fix
Check if increasing all indexes by a fixed amount fixes the problem. Only tries to find a solution if there are 3 or more sequence positions indicated.
Example request
Example response (a list of possible solutions that is empty if no solution exists):
Priority
In the allele fixing pipeline the highest priority is old_coords fix, then histone, then multi_shift. So only the first one that gives a solution should be kept.
How to display the possible solution to the user