ortho_ranker/config.missing_expression_id.yaml at main · LijieZhou-coder/ortho_ranker · GitHub

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project:
  name: missing_expression_id_run
  mode: strict
  goal: high_precision
  allow_no_unique_hit: true
  return_single_best_only_if_unique: true

paths:
  query_fasta: ./test_data/query_test.fa

  target_proteome: ./test_data/target_test.fa
  target_blastdb_prefix: ./test_data/blastdb/target_test_db

  reference_proteome: ./test_data/target_test.fa
  reference_blastdb_prefix: ./test_data/blastdb/target_test_db

  pfam_db: /path/to/Pfam-A.hmm
  output_dir: results/missing_expression_id_run

thresholds:
  evalue_cutoff: 1.0e-5
  query_cov_cutoff: 0.70
  subject_cov_cutoff: 0.70
  reciprocal_query_cov_cutoff: 0.70
  reciprocal_subject_cov_cutoff: 0.70
  top1_ratio_cutoff: 0.90
  breakpoint_drop_cutoff: 0.10
  breakpoint_median_multiplier: 2.0
  reciprocal_top_gap_cutoff: 0.05
  max_hits_to_keep: 10

domain:
  require_core_domain: true
  require_domain_architecture_match: true
  allow_domain_partial_for_single_best: false

family:
  mode: simple
  rationale: minimal synthetic test

expression:
  enabled: true
  matrix_file: test_data/expression/expression_missing_id.tsv
  gene_id_column: gene_id
  expression_metric: FPKM
  target_samples:
    - petal_1
    - petal_2
  background_samples:
    - leaf_1
    - leaf_2
  ranking_strategy: combined
  min_expression_threshold: 0.0
  include_no_valid_hit: true
  pseudocount: 1.0