# =============================================================================
# config.yaml — Genome Dataset Pre-processing Configuration
# =============================================================================

# Root directory containing all species folders.
# Expected layout: {data_root}/{species}/{assembly}/{species}_{annotation}_genomic.fna
#                                                   {species}_{annotation}.gff3
data_root: /share/kuleshov/emm392/mammal_genomes/

# Where to write the final HuggingFace DatasetDict (saved with save_to_disk).
output_dir: "./output"

# Where to cache processed annotation files
cache_dir: ".cache"

# ---------------------------------------------------------------------------
# Sliding-window parameters
# ---------------------------------------------------------------------------
chunk_size: 12_000       # Length of each sequence chunk in base pairs
stride: 12_000           # Step size between consecutive chunks (256 = 50% overlap for chunk of 512)
                      # Set stride == chunk_size for non-overlapping chunks

# ---------------------------------------------------------------------------
# CDS flanking regions
# ---------------------------------------------------------------------------
# Extra bases to include BEFORE the CDS start (upstream, on the feature strand)
flank_upstream_bp: 10_000
# Extra bases to include AFTER the CDS end (downstream, on the feature strand)
flank_downstream_bp: 10_000

# max percentage of N's allowed in a given sequence
max_n_perc: 0.25 

# ---------------------------------------------------------------------------
# Species selection & validation split
# ---------------------------------------------------------------------------
# Only species listed here are processed — everything else in data_root is
# ignored. Each entry requires:
#   - name          : matches the directory name exactly under data_root
#   - val_chromosome: contig/chromosome ID to hold out for validation.
#                     Must match the FASTA header exactly (first word after ">").
#                     Tip: grep "^>" your_file.fna | head  to list available IDs.
#
# train species — ALL chromosomes go to train except val_chromosome
# validation species — same rule applies; val_chromosome goes to validation,
#                      remaining chromosomes go to train
#
# If you want a species to contribute ONLY to train (no val chrom), set
# val_chromosome to null.

species:
  train:
    - name: "Homo_sapiens"
      val_chromosome: "NC_000008.11"    # hold out chr8

    - name: "Mus_musculus"
      val_chromosome: "NC_000070.7"     # hold out chr3

    - name: "Pan_troglodytes"
      val_chromosome: "NC_072404.2"     # hold out chr6

    # Add more training species here:
    # - name: "rattus_norvegicus"
    #   val_chromosome: "NC_005100.4"

  validation:
    # Species listed here follow the same rule: val_chromosome → validation,
    # all other chromosomes → train. Use this section if you want to keep
    # certain species exclusively (or primarily) for evaluation bookkeeping.
    # Most users will leave this empty and rely on val_chromosome above.
    #
    # - name: "danio_rerio"
    #   val_chromosome: "NC_007112.7"

# ---------------------------------------------------------------------------
# Misc
# ---------------------------------------------------------------------------
shuffle: False    # Shuffle the training set after building
seed: 42