##README: Guide to python scripts ##PROCESSING MHC FILES FOR jMHC Barcodes-min.py # A script to extract barcodes from fasta sequence headers and insert at the beginning of reads. # Used to import MHC data into the software jMHC. ##PROCESSING STACKS DATA FOR PROVEAN ANALYSIS (DELETERIOUS MUTATIONS) make_fasta_with_all_alleles.py # A script to make a fasta file for each allele using the Stacks catalog.fa file and a VCF file. parse_blast_results_best_align_delet_mut_consensus_seqs.py # A script to parse blast alignments to retain matches with >40 amino acids and % identity >90% as well as the # match with the highest % identity if there were multiple matches. pull_seqs_to_translate_consensus_blast.py # A script to translate aligned sequences to protein coding sequences. generate_provean_files.py # A script to convert protein sequences with non-synonymous mutations into PROVEAN input files. parse_provean_output.py # A script to parse the PROVEAN results output.