| # ============================================================================= | |
| # 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 | |