#!/usr/bin/env bash # ============================================================ # run_config.sh — MASTER CONFIGURATION for SATURN_Mnemi # # 5-species immune integration: # Mlei Mnemiopsis leidyi (ctenophore) # Cgig Crassostrea gigas (oyster) # Spur Strongylocentrotus purpuratus (sea urchin) # Crob Ciona robusta (tunicate) # Drer Danio rerio (zebrafish) # # SOURCE at the top of every pipeline script: # source "$(dirname "$0")/run_config.sh" # ============================================================ # ------------------------------------------------------------ # TOP-LEVEL PATHS # ------------------------------------------------------------ export BASE="/scratch/dark_genes/SATURN_Mnemi" export SCRIPTS_DIR="${BASE}/scripts" export SATURN_DIR="${HOME}/SATURN" # ------------------------------------------------------------ # SATURN SCRIPT PATHS # ------------------------------------------------------------ export SATURN_TRAIN="${SATURN_DIR}/train-saturn.py" export ESM_EXTRACT="${SATURN_DIR}/protein_embeddings/extract.py" export ESM_FILTER="${SATURN_DIR}/protein_embeddings/filter_proteins_with_embeddings.py" export ESM_CONVERT="${SATURN_DIR}/protein_embeddings/convert_protein_embeddings_to_gene_embeddings.py" export ESM_MODEL="esm1b_t33_650M_UR50S" # ------------------------------------------------------------ # ACTIVE SPECIES LIST # ------------------------------------------------------------ export SPECIES_LIST=("Mlei" "Cgig" "Spur" "Crob" "Drer") # ------------------------------------------------------------ # PER-SPECIES CONFIGURATION # Call: get_species_config # Sets: H5AD_IN, H5AD_LABEL_COL, PROTEOME_FASTA, GTF, EMB_STRATEGY # ------------------------------------------------------------ get_species_config() { SP="$1" case "${SP}" in Mlei) # Mnemiopsis leidyi — ctenophore # var_names: g-XXXX (hyphen; FASTA renamed to match) # .X: raw counts H5AD_IN="${BASE}/00_source_data/Mlei/Mlei_raw.h5ad" H5AD_LABEL_COL="seurat_clusters" PROTEOME_FASTA="${BASE}/01_proteomes/Mlei/Mlei.protein.faa" GTF="" EMB_STRATEGY="direct" ;; Cgig) # Crassostrea gigas — Pacific oyster (hemocytes only) # var_names: LOC###### (NCBI RefSeq) # GTF: LOC→XP_ mapping H5AD_IN="${BASE}/00_source_data/Cgig/Cgig.hemocytes.h5ad" H5AD_LABEL_COL="seurat_clusters" PROTEOME_FASTA="${BASE}/01_proteomes/Cgig/Cgig.protein.faa" GTF="${BASE}/01_proteomes/Cgig/Cgig.genomic.gtf" EMB_STRATEGY="gtf_loc_to_xp" ;; Spur) # Strongylocentrotus purpuratus — sea urchin (full dataset) # var_names: LOC###### (NCBI RefSeq) # GTF: LOC→XP_ mapping H5AD_IN="${BASE}/00_source_data/Spur/Spur_full.h5ad" H5AD_LABEL_COL="cell_type" PROTEOME_FASTA="${BASE}/01_proteomes/Spur/Spur_5.0.protein.faa" GTF="${BASE}/01_proteomes/Spur/Spur_5.0.genomic.gtf" EMB_STRATEGY="gtf_loc_to_xp" ;; Crob) # Ciona robusta — tunicate blood (Scully et al. 2025, GSE296253) # var_names: KY21.Chr1.N (Ghost DB KY21 gene models) # FASTA headers: KY21.Chr1.N.v1.nonSL19-1 → strip suffix H5AD_IN="${BASE}/00_source_data/Crob/Crob_blood.h5ad" H5AD_LABEL_COL="cell_type" PROTEOME_FASTA="${BASE}/01_proteomes/Crob/Crob_KY21_ghost.faa" GTF="" EMB_STRATEGY="direct_strip_suffix" ;; Drer) # Danio rerio — zebrafish spleen immune cells (Jiao et al. 2024, GSE186158) # var_names: gene symbols (ptpn12, cd79b, etc.) # GTF: symbol→ENSDARG→ENSDARP mapping (Ensembl GRCz11) H5AD_IN="${BASE}/00_source_data/Drer/Drer.h5ad" H5AD_LABEL_COL="seurat_clusters" PROTEOME_FASTA="${BASE}/01_proteomes/Drer/Drer.protein.faa" GTF="${BASE}/01_proteomes/Drer/Drer.genomic.gtf" EMB_STRATEGY="gtf_symbol_to_ensdarg" ;; Dmel) # Drosophila melanogaster -- larval circulating hemocytes (Cattenoz et al. 2020, E-MTAB-8698 NI) # var_names: FlyBase FBgn IDs. Proteome: Ensembl r113 BDGP6 pep.all (headers carry gene:FBgn...) # Prepared by 07d_prepare_Dmel_Hsap.sh (no 00_source_data copy; H5AD_IN points at the prepared file) H5AD_IN="${BASE}/02_processed_h5ad/Dmel_saturn.h5ad" H5AD_LABEL_COL="cell_type" PROTEOME_FASTA="$(ls ${BASE}/01_proteomes/Dmel/Drosophila_melanogaster.*.pep.all.fa 2>/dev/null | head -1)" GTF="" EMB_STRATEGY="ensembl_gene_id" ;; Hsap) # Homo sapiens -- CellTypist cross-tissue immune atlas, 10x 3' v3 subset (Dominguez Conde et al. 2022) # var_names: Ensembl ENSG IDs. Proteome: Ensembl r113 GRCh38 pep.all (headers carry gene:ENSG....version) # Prepared by 07d_prepare_Dmel_Hsap.sh H5AD_IN="${BASE}/02_processed_h5ad/Hsap_saturn.h5ad" H5AD_LABEL_COL="cell_type" PROTEOME_FASTA="${BASE}/01_proteomes/Hsap/Homo_sapiens.GRCh38.pep.all.fa" GTF="" EMB_STRATEGY="ensembl_gene_id" ;; *) echo "ERROR: Unknown species '${SP}'. Add a config block to run_config.sh." >&2 return 1 ;; esac export H5AD_IN H5AD_LABEL_COL PROTEOME_FASTA GTF EMB_STRATEGY # Derived paths — computed from SP after case block export H5AD_SATURN="${BASE}/02_processed_h5ad/${SP}_saturn.h5ad" export EMB_DIR="${BASE}/03_embeddings/${SP}" export EMB_GENES_TXT="${EMB_DIR}/${SP}_genes.txt" export EMB_FILTERED_FASTA="${EMB_DIR}/${SP}_filtered.faa" export EMB_PT_DIR="${EMB_DIR}/${SP}_pt_embeddings" export EMB_MAP_JSON="${EMB_DIR}/${SP}_gene_to_protein.json" export EMB_FILTERED_JSON="${EMB_DIR}/${SP}_gene_to_protein.filtered.json" export EMB_H5="${EMB_DIR}/${SP}_gene_embeddings.h5" export EMB_PT="${EMB_DIR}/${SP}_gene_embeddings.pt" export EMB_LOC_MAP_TSV="${EMB_DIR}/${SP}_gene_to_protein.tsv" } # ------------------------------------------------------------ # SATURN HYPERPARAMETERS # ------------------------------------------------------------ export K_MACROGENES=3000 export MACROGENE_SEED=42 export HV_GENES=8000 # Post-SATURN UMAP (settled: no StandardScaler, PCA5, cosine) export UMAP_N_PCS=5 export UMAP_METRIC="cosine" export UMAP_N_NEIGHBORS=80 export UMAP_MIN_DIST=0.10 export LEIDEN_RESOLUTION=1.2 export MIN_CELLS_PER_SPECIES=50 # min Mlei cells per cluster # MIN-N macrogene filters — both run in postSATURN step export MIN_N_FILTERS="1 3 5" # space-separated; runs MIN3-of-5 and MIN5-of-5 # ------------------------------------------------------------ # CONDA ENVIRONMENT # ------------------------------------------------------------ export CONDA_ENV="saturn_protein"