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7f316fe 12fea4a | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 | """Repo-root path helpers. All scripts should import this instead of hardcoding hosts."""
from __future__ import annotations
import os
import shutil
import sys
from pathlib import Path
REPO_ROOT = Path(__file__).resolve().parent
def add_repo_to_sys_path() -> Path:
root = str(REPO_ROOT)
if root not in sys.path:
sys.path.insert(0, root)
return REPO_ROOT
def resolve_path(path: str | Path) -> Path:
p = Path(path).expanduser()
if p.is_absolute():
return p
return (REPO_ROOT / p).resolve()
def peptiverse_root() -> Path:
env = os.environ.get("PEPTIVERSE_ROOT")
if env:
root = Path(env).expanduser().resolve()
else:
root = (REPO_ROOT.parent / "PeptiVerse").resolve()
if not root.is_dir():
raise FileNotFoundError(
"PeptiVerse was not found. Clone it first and either place it next "
f"to this repo ({REPO_ROOT.parent / 'PeptiVerse'}) or set PEPTIVERSE_ROOT.\n"
" git clone https://huggingface.co/ChatterjeeLab/PeptiVerse"
)
return root
def mafft_path() -> str:
env = os.environ.get("MAFFT_PATH")
if env:
if Path(env).is_file() and os.access(env, os.X_OK):
return env
raise FileNotFoundError(f"MAFFT_PATH is set but not an executable: {env}")
found = shutil.which("mafft")
if found:
return found
raise FileNotFoundError(
"MAFFT was not found on PATH. Install it and make sure `mafft` is "
"executable, or set MAFFT_PATH to the binary. GFP FPredX oracles require MAFFT."
)
def smiles_vocab_files() -> tuple[Path, Path]:
return (
REPO_ROOT / "smiles_tokenizer" / "new_vocab.txt",
REPO_ROOT / "smiles_tokenizer" / "new_splits.txt",
)
def selfies_vocab_path() -> Path:
return REPO_ROOT / "smiles_tokenizer" / "selfies_vocab.json"
# --- Cas9 ---------------------------------------------------------------
def protein2pam_root() -> Path:
"""Root of the protein2pam package (provides the custom ESM loader).
Weights come from the Hub ("Profluent-Bio/protein2pam-cas9_full"); this is
only the Python package that defines the model class.
"""
env = os.environ.get("PROTEIN2PAM_ROOT")
root = Path(env).expanduser().resolve() if env else (REPO_ROOT / "cas9" / "protein2pam")
if not root.is_dir():
raise FileNotFoundError(
"protein2pam was not found. Install it next to the Cas9 code at "
f"{REPO_ROOT / 'cas9' / 'protein2pam'} or set PROTEIN2PAM_ROOT.\n"
" pip install protein2pam==0.2.0"
)
return root
def cas_predictor_root() -> Path:
"""Root of the cas_predictor package (model.py + lightning_module.py)."""
env = os.environ.get("CAS_PREDICTOR_ROOT")
root = Path(env).expanduser().resolve() if env else (REPO_ROOT / "cas9" / "cas_predictor")
if not root.is_dir():
raise FileNotFoundError(
"cas_predictor was not found. Place it at "
f"{REPO_ROOT / 'cas9' / 'cas_predictor'} or set CAS_PREDICTOR_ROOT."
)
return root
def cas9_classifier_ckpt() -> Path:
"""Cas9-likeness classifier checkpoint (hard constraint + objective)."""
env = os.environ.get("CAS9_CLASSIFIER_CKPT")
p = resolve_path(env) if env else (REPO_ROOT / "cas9" / "classifier_ckpt" / "last.ckpt")
if not p.is_file():
raise FileNotFoundError(
f"Cas9 classifier checkpoint not found at {p}. Download it into "
"cas9/classifier_ckpt/ or set CAS9_CLASSIFIER_CKPT."
)
return p
def cas9_classifier_config() -> Path | None:
"""Optional classifier config; None falls back to the ckpt hyper_parameters."""
env = os.environ.get("CAS9_CLASSIFIER_CONFIG")
if env:
return resolve_path(env)
default = REPO_ROOT / "cas9" / "classifier_ckpt" / "config.yaml"
return default if default.is_file() else None
def cas9_hmm_db(name: str) -> Path:
"""HMM database under cas9/hmm/ (e.g. 'cas9_domain_detector_RuvCmix.hmm')."""
env = os.environ.get("CAS9_HMM_DIR")
root = Path(env).expanduser().resolve() if env else (REPO_ROOT / "cas9" / "hmm")
p = root / name
if not p.is_file():
raise FileNotFoundError(
f"HMM database {name} not found at {p}. Place it in cas9/hmm/ or set CAS9_HMM_DIR."
)
return p
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