170 lines
6.4 KiB
Python
Executable File
170 lines
6.4 KiB
Python
Executable File
from pathlib import Path
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from openpyxl import Workbook
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from apps.cli import run_identify as identify
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def _write_config(path: Path, rows: list[list[str]]) -> None:
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wb = Workbook()
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ws = wb.active
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ws.title = "config"
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ws.append([
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"Original_File_Name",
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"Species_Code",
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"Species_Name",
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"Gene_Family",
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"File_Type",
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"Ref",
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"Species_Role",
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"File_Scope",
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"Reference_Use",
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])
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for row in rows:
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ws.append(row)
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wb.save(path)
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def test_collect_reference_files_ignores_family_pep_filename_without_config(tmp_path):
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ref = tmp_path / "At.SPL.pep.fasta"
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ref.write_text(">AtSPL1\nMAAA\n", encoding="utf-8")
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references = identify.collect_reference_files(tmp_path, gene_family="SPL")
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assert references == []
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def test_collect_reference_files_uses_config_family_pep_for_identify_blast(tmp_path):
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ref = tmp_path / "At.SPL.pep.fasta"
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ref.write_text(">AtSPL1\nMAAA\n", encoding="utf-8")
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_write_config(
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tmp_path / "config.xlsx",
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[[
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"At.SPL.pep.fasta",
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"At",
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"Arabidopsis thaliana",
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"SPL",
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"family_pep",
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"TRUE",
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"seed_reference",
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"known_family",
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"identify_blast",
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]],
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)
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references = identify.collect_reference_files(tmp_path, gene_family="SPL")
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assert len(references) == 1
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assert references[0]["species"] == "At"
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assert references[0]["source"] == "config.xlsx"
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assert Path(references[0]["path"]) == ref.resolve()
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def test_parse_blast_outfmt6_uses_sseqid_for_target_candidates(tmp_path):
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blast_out = tmp_path / "Pm.blast.At.out"
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blast_out.write_text(
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"AtNAC001\tPmNAC001\t45.0\t100\t0\t0\t1\t100\t5\t104\t1e-40\t180\t120\t130\n"
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"AtNAC002\tPmNAC002\t31.0\t90\t0\t0\t1\t90\t10\t99\t1e-06\t90\t110\t120\n"
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"AtNAC003\tPmNAC003\t30.0\t90\t0\t0\t1\t90\t10\t99\t1e-20\t100\t110\t120\n"
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"AtNAC004\tPmNAC004\t55.0\t90\t0\t0\t1\t90\t10\t99\t1e-03\t100\t110\t120\n",
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encoding="utf-8",
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)
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ids, evidence = identify.parse_blast_outfmt6_target_hits(blast_out, evalue=1e-5)
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assert ids == {"PmNAC001", "PmNAC002"}
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assert "AtNAC001" not in ids
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assert evidence["PmNAC001"]["query_ids"] == ["AtNAC001"]
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assert evidence["PmNAC001"]["best_evalue"] == 1e-40
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def test_multi_reference_blast_unions_target_sseqids_and_query_support(monkeypatch, tmp_path):
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output_dir = tmp_path / "identify" / "Pm"
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analysis_dir = output_dir / "analysis"
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analysis_dir.mkdir(parents=True)
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pep = tmp_path / "Pm.pep.fasta"
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pep.write_text(">PmNAC001\nMAAA\n>PmNAC002\nMBBB\n", encoding="utf-8")
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at_ref = tmp_path / "At.NAC.pep.fasta"
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os_ref = tmp_path / "Os.NAC.pep.fasta"
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at_ref.write_text(">AtNAC001\nMAAA\n", encoding="utf-8")
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os_ref.write_text(">OsNAC009\nMBBB\n", encoding="utf-8")
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monkeypatch.setattr(identify, "cleanup_current_blast_intermediates", lambda analysis_dir, prefix: None)
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monkeypatch.setattr(
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identify,
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"build_target_proteome_blast_db",
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lambda analysis_dir, pep_file: {
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"status": "success",
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"target_database_input": str(pep_file.resolve()),
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"target_database_role": "target_proteome",
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"target_db_prefix": str((analysis_dir / "blast_db.target_proteome").resolve()),
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"target_database_files": [str((analysis_dir / "blast_db.target_proteome.pin").resolve())],
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},
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)
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def fake_run_blast_analysis(**kwargs):
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label = kwargs["reference_label"]
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if label == "At":
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return {
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"status": "success",
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"reference_label": "At",
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"query_file": str(at_ref.resolve()),
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"query_role": "reference_family_pep",
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"target_database_input": str(pep.resolve()),
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"target_database_role": "target_proteome",
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"target_db_prefix": str((analysis_dir / "blast_db.target_proteome").resolve()),
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"target_database_files": [],
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"candidate_id_column": "sseqid",
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"blast_output": str((analysis_dir / "Pm.blast.At.out").resolve()),
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"ids_file": str((analysis_dir / "Pm.blast.At.ids").resolve()),
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"members": 1,
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"ids": ["PmNAC001"],
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"evidence_by_gene": {"PmNAC001": {"query_ids": ["AtNAC001"], "best_evalue": 1e-40, "best_bitscore": 180.0}},
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}
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return {
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"status": "success",
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"reference_label": "Os",
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"query_file": str(os_ref.resolve()),
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"query_role": "reference_family_pep",
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"target_database_input": str(pep.resolve()),
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"target_database_role": "target_proteome",
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"target_db_prefix": str((analysis_dir / "blast_db.target_proteome").resolve()),
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"target_database_files": [],
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"candidate_id_column": "sseqid",
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"blast_output": str((analysis_dir / "Pm.blast.Os.out").resolve()),
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"ids_file": str((analysis_dir / "Pm.blast.Os.ids").resolve()),
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"members": 2,
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"ids": ["PmNAC001", "PmNAC002"],
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"evidence_by_gene": {
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"PmNAC001": {"query_ids": ["OsNAC009"], "best_evalue": 1e-20, "best_bitscore": 140.0},
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"PmNAC002": {"query_ids": ["OsNAC010"], "best_evalue": 1e-25, "best_bitscore": 150.0},
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},
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}
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monkeypatch.setattr(identify, "run_blast_analysis", fake_run_blast_analysis)
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result = identify.run_multi_reference_blast_analysis(
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input_dir=tmp_path,
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output_dir=output_dir,
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prefix="Pm",
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references=[{"label": "At", "path": str(at_ref)}, {"label": "Os", "path": str(os_ref)}],
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pep_file=pep,
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evalue=1e-5,
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)
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assert Path(result["ids_file"]).read_text(encoding="utf-8").splitlines() == ["PmNAC001", "PmNAC002"]
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matrix = Path(result["source_matrix"]).read_text(encoding="utf-8").splitlines()
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assert matrix[0].split("\t") == [
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"gene_id",
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"blast_reference_sources",
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"blast_reference_count",
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"blast_query_ids",
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"best_evalue",
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"best_bitscore",
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]
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assert "PmNAC001\tAt;Os\t2\tAtNAC001;OsNAC009\t1e-40\t180.0" in matrix
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assert "PmNAC002\tOs\t1\tOsNAC010\t1e-25\t150.0" in matrix
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assert result["blast_database_role"] == "target_proteome"
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assert result["blast_query_role"] == "reference_family_pep"
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assert result["blast_candidate_id_column"] == "sseqid"
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