trainer_batcher_example.yml

shell_script: ./start_ahrd_batched.sh
ahrd_call: "java -Xmx2048m -cp ./dist/ahrd.jar ahrd.controller.Trainer #batch#"
proteins_fasta: ./test/resources/proteins.fasta
references_fasta: ./test/resources/references.fasta
no_start_positions_in_parameter_space: 1024
batch_ymls_dir: ./trainer_batch_ymls
output_dir: ./trainer_results
blast_dbs:
  swissprot:
    file: ./test/resources/swissprot_blast8_tabular.txt
    database: ./test/resources/swissprot_blast_db.fasta
    blacklist: ./test/resources/blacklist_descline.txt
    filter: ./test/resources/filter_descline_sprot.txt
    token_blacklist: ./test/resources/blacklist_token.txt

  trembl:
    file: ./test/resources/trembl_blast8_tabular.txt
    database: ./test/resources/trembl_blast_db.fasta
    blacklist: ./test/resources/blacklist_descline.txt
    filter: ./test/resources/filter_descline_trembl.txt
    token_blacklist: ./test/resources/blacklist_token.txt

  tair:
    file: ./test/resources/tair_blast8_tabular.txt
    database: ./test/resources/tair_blast_db.fasta
    fasta_header_regex: "^>(?<accession>[aA][tT][0-9mMcC][gG]\\d+(\\.\\d+)?)\\s+\\|[^\\|]+\\|\\s+(?<description>[^\\|]+)(\\s*\\|.*)?$"
    short_accession_regex: "^(?<shortAccession>.+)$"
    blacklist: ./test/resources/blacklist_descline.txt
    filter: ./test/resources/filter_descline_tair.txt
    token_blacklist: ./test/resources/blacklist_token.txt