This tool can analyze amino acid frequency in alignment files of a given position of the reference sequence.
For basic usage of finding amino acid frequency of a specific position like 116:
python HLA.py -i Data/B_prot.txt -p 116
This tool uses a alignment file in IPD-IMGT/HLA 3.54.0 format as input.
--position,-p: if set analyzes the amino acid frequency of specified position of the reference sequence.
--count,-c: if set the tool will output a histogram of common variations found per position.
--cluster,-cl: if set the amino-acid histogram will be clustered together based on a shared property.
Currently class and polarity are the options available.
--protein_threshold, -pt: if set changes the threshold of minimum amount of proteins
needed before they are considered expressed by the specific amino acid at the specified location.
--threshold_test, -tt: if set a plot will be generated showing the amount of protein_ids includes
for each set threshold up to 200,as well as the amount of duplicate ids shared between amino acids.