Upload config.yaml with huggingface_hub

config.yaml

@@ -0,0 +1,79 @@
+# =============================================================================
+# 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