AgMM and AAMM Summary Tables Update

[alyspayn]

Fix the old scripts that need to be updated with new FIBERS 2.0 data. https://github.com/lgragert/srtr-impute-pubsaf2306/blob/main/FIBERS_AgMM_summary_table.py https://github.com/lgragert/srtr-impute-pubsaf2306/blob/main/FIBERS_AAMM_summary_table.py

1. The old scripts need to be in terms of the SRTR_AA_MM_9locmatrix*.txt.gz files (change lines 137-147) and new population groups (change line 130 for that).
2. Create a config file of the high and low-risk groups found by FIBERS so that it is not hard-coded into the scripts.
   • The low risk group is when there are 0 AA-MM and high risk group is when there are >=1 AA-MM from the AA-MM found from FIBERS bins. (lines 160-169 is where the hardcode is for the high and low risk FIBERS group).
3. The same or different config file can also be used for the AA-MM script, where it will let us look at the top bins created by FIBERS (lines 255-313). You also have to change the population groups (line 236) and file name to be the matrix files (line 218).

[alyspayn]

The hardcoding is no longer within the scripts and takes in the config file amino_acids.json. However some issues still persist. The matrix files are missing the AgMM for DQ, so the scripts cannot run fully without it. Also thee population groups are different in the file and need to be mapped to the names that we want.

[JK4800]

• Added DQ Ag MM category for REC_DQ_MM_EQUIV_CUR in the SRTR matrix files -- scripts now call in new files SRTR_AA_MM_9loc_matrixDQAg*.txt.gz
• New population groups are handled, keeping the same population codes to maintain readability -- non-main population groups have been combined into "OTHER"
• Integrated FIBERS 2.0 output file so that it updates the config file with the new single AAMM bin features within the scripts themselves -- still using amino_acids.json