Initial commit: Chai-1 protein structure prediction pipeline for WES

- Nextflow pipeline using chai1 Docker image from Harbor
- S3-based input/output paths (s3://omic/eureka/chai-lab/)
- GPU-accelerated protein folding with MSA support

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

tests/test_parsing.py

@@ -0,0 +1,79 @@
+# Copyright (c) 2024 Chai Discovery, Inc.
+# Licensed under the Apache License, Version 2.0.
+# See the LICENSE file for details.
+
+from pathlib import Path
+from tempfile import TemporaryDirectory
+
+from chai_lab.data.parsing.fasta import read_fasta
+from chai_lab.data.parsing.input_validation import (
+    constituents_of_modified_fasta,
+    identify_potential_entity_types,
+)
+from chai_lab.data.parsing.structure.entity_type import EntityType
+
+from .example_inputs import example_dna, example_ligands, example_proteins, example_rna
+
+
+def test_simple_protein_fasta():
+    parts = constituents_of_modified_fasta("RKDES")
+    assert parts is not None
+    assert all(x == y for x, y in zip(parts, ["R", "K", "D", "E", "S"]))
+
+
+def test_modified_protein_fasta():
+    parts = constituents_of_modified_fasta("(KCJ)(SEP)(PPN)(B3S)(BAL)(PPN)KX(NH2)")
+    assert parts is not None
+    expected = ["KCJ", "SEP", "PPN", "B3S", "BAL", "PPN", "K", "X", "NH2"]
+    assert all(x == y for x, y in zip(parts, expected))
+
+
+def test_rna_fasta():
+    seq = "ACUGACG"
+    parts = constituents_of_modified_fasta(seq)
+    assert parts is not None
+    assert all(x == y for x, y in zip(parts, seq))
+
+
+def test_dna_fasta():
+    seq = "ACGACTAGCAT"
+    parts = constituents_of_modified_fasta(seq)
+    assert parts is not None
+    assert all(x == y for x, y in zip(parts, seq))
+
+
+def test_parsing():
+    for ligand in example_ligands:
+        assert EntityType.LIGAND in identify_potential_entity_types(ligand)
+
+    for protein in example_proteins:
+        assert EntityType.PROTEIN in identify_potential_entity_types(protein)
+
+    for dna in example_dna:
+        assert EntityType.DNA in identify_potential_entity_types(dna)
+
+    for rna in example_rna:
+        assert EntityType.RNA in identify_potential_entity_types(rna)
+
+
+def test_fasta_parsing():
+    test_string = """>foo\nRKDES\n>bar\nKEDESRRR"""
+    with TemporaryDirectory() as tmpdir:
+        fa_file = Path(tmpdir) / "test.fasta"
+        fa_file.write_text(test_string)
+        records = read_fasta(fa_file)
+
+    assert len(records) == 2
+    assert records[0].header == "foo"
+    assert records[0].sequence == "RKDES"
+    assert records[1].header == "bar"
+    assert records[1].sequence == "KEDESRRR"
+
+
+def test_smiles_parsing():
+    smiles = ">smiles\nCc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C"
+    with TemporaryDirectory() as tmpdir:
+        fa_file = Path(tmpdir) / "test.fasta"
+        fa_file.write_text(smiles)
+        records = read_fasta(fa_file)
+    assert len(records) == 1