fix requirements

ntv3_tracks_pipeline.py

@@ -9,11 +9,6 @@ import torch
 from transformers import AutoConfig, AutoModel, AutoTokenizer
 from transformers.pipelines import Pipeline
 
-try:
-    from pyfaidx import Fasta
-except Exception:
-    Fasta = None
-
 try:
     import requests
 except Exception:
@@ -211,39 +206,6 @@ def _get_dna_sequence(assembly: str, chrom: str, start: int, end: int) -> str:
     return seq
 
 
-def _ensure_fasta_for_assembly(assembly: str, cache_dir: str | Path) -> Path:
-    """
-    Download <assembly>.fa.gz, decompress to <assembly>.fa, return the .fa path.
-    pyfaidx works reliably on uncompressed FASTA.
-    """
-    cache_dir = Path(cache_dir).expanduser().resolve()
-    cache_dir.mkdir(parents=True, exist_ok=True)
-
-    fa_path = cache_dir / f"{assembly}.fa"
-    gz_path = cache_dir / f"{assembly}.fa.gz"
-
-    if fa_path.exists():
-        return fa_path
-
-    # This function is deprecated - use _get_dna_sequence with API instead
-    raise ValueError(
-        f"FASTA file download is no longer supported for assembly='{assembly}'. "
-        f"Please use _get_dna_sequence() with API-based sequence fetching instead."
-    )
-
-    import gzip
-
-    print(f"Decompressing {gz_path} -> {fa_path}")
-    with gzip.open(gz_path, "rb") as fin, open(fa_path, "wb") as fout:
-        while True:
-            chunk = fin.read(1024 * 1024)
-            if not chunk:
-                break
-            fout.write(chunk)
-
-    return fa_path
-
-
 def _pick_device(device: str | int | torch.device) -> torch.device:
     # Handle torch.device objects
     if isinstance(device, torch.device):