dvc.yaml

stages:
  run_msa:
    cmd: python scripts/run_msa.py
    params:
      - use_msa
      - msa_creation.msa_mode

      # if msa_mode is starting_sequences
      - msa_creation.starting_sequences.prealigned
      - msa_creation.starting_sequences.add_training_sequences
      - msa_creation.starting_sequences.activity_targets
      - msa_creation.starting_sequences.activity_threshold

      # if msa_mode is jackhmmer
      - msa_creation.jackhmmer.seqdb
      - msa_creation.jackhmmer.iterations
      - msa_creation.jackhmmer.domain_threshold
      - msa_creation.jackhmmer.sequence_threshold
      - msa_creation.jackhmmer.use_bitscores
      - msa_creation.jackhmmer.sequence_identity_filter
      - msa_creation.jackhmmer.theta
      - msa_creation.jackhmmer.minimum_column_coverage
      - msa_creation.jackhmmer.minimum_sequence_coverage
      - msa_creation.jackhmmer.cpus
      - msa_creation.jackhmmer.mx
    deps:
      - data/starting_sequences.fa
      - data/starting_sequences.a2m
      - data/experimental_data.csv
      - data/wt.fa
      - scripts/run_msa.py
    outs: 
      - data/run_msa/
    metrics:
      - data/metrics/run_msa.json:
          cache: false
  process_msa:
    cmd: python scripts/process_msa.py
    params:
      - msaprocessing.theta
      - msaprocessing.use_weights
      - msaprocessing.preprocess
      - msaprocessing.threshold_sequence_frac_gaps
      - msaprocessing.threshold_focus_cols_frac_gaps
      - msaprocessing.remove_sequences_with_indeterminate_AA_in_focus_cols
      - msaprocessing.additional_weights
    deps:
      - data/run_msa/
      - scripts/process_msa.py
      - data/wt.fa
    outs:
      - data/process_msa/
    metrics:
      - data/metrics/process_msa.json:
          cache: false