feat: add more species

app.py

@@ -521,21 +521,12 @@ _init_bigwig_selected = [tid for tid in DEFAULT_BIGWIG_TRACKS if tid in _init_bi
 # Filter default BED elements to only those available
 _init_bed_selected = [elem for elem in DEFAULT_BED_ELEMENTS if elem in _init_bed]
 
-# Default coordinates per species
-DEFAULT_COORDS = {
-    "human": {"chrom": "chr19", "start": 6_700_000, "end": 6_831_072},
-    "mouse": {"chrom": "chr1", "start": 100_000, "end": 200_000},
-    "drosophila_melanogaster": {"chrom": "chr2L", "start": 1_000_000, "end": 2_000_000},
-}
-
-# Get default coordinates for default species
-_default_coords = DEFAULT_COORDS.get(DEFAULT_SPECIES, DEFAULT_COORDS["human"])
-
 # Default coordinates per species
 DEFAULT_COORDS = {
     "human": {"chrom": "chr19", "start": 6_700_000, "end": 6_831_072},
     "mouse": {"chrom": "chr1", "start": 0, "end": 32_768},
     "drosophila_melanogaster": {"chrom": "chr2L", "start": 0, "end": 32_768},
+    "arabidopsis_thaliana": {"chrom": "chr1", "start": 0, "end": 32_768},
 }
 
 # Get default coordinates for default species
@@ -552,6 +543,9 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
     Predict and visualize functional genomics signals directly from DNA using
     <strong>Nucleotide Transformer v3</strong>.
   </p>
+  <p style="margin-top: 8px; font-size: 0.95rem; opacity: 0.85;">
+    <strong>Currently available species:</strong> Human, Mouse, Drosophila melanogaster, Arabidopsis thaliana, Gorilla
+  </p>
 </div>
 
 <div class="intro-grid">
@@ -584,7 +578,7 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
 
 <div class="intro-tip">
   <span class="intro-tip-icon">💡</span>
-  <span><strong>Tip:</strong> The demo include default settings that you can use to get started, taking ~ 1 minute to run.</span>
+  <span><strong>Tip:</strong> The demo includes default settings that you can use to get started, taking ~ 1 minute to run.</span>
 </div>
 
 </div>
@@ -619,7 +613,7 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
     
     with gr.Row():
         species = gr.Dropdown(
-            ["human", "mouse", "drosophila_melanogaster"],
+            ["human", "mouse", "drosophila_melanogaster", "arabidopsis_thaliana", "gorilla_gorilla"],
             value=DEFAULT_SPECIES,
             label="Species",
         )

ntv3_tracks_pipeline.py

@@ -61,6 +61,20 @@ ASSEMBLY_TO_SPECIES = {
 }
 SPECIES_TO_ASSEMBLY = {v: k for k, v in ASSEMBLY_TO_SPECIES.items()}
 
+# ---------------------------------------------------------------------
+# Assembly -> API URL template mapping
+# ---------------------------------------------------------------------
+# Default API URL template (UCSC format) that works for most species
+DEFAULT_API_URL_TEMPLATE = "https://api.genome.ucsc.edu/getData/sequence?genome={assembly};chrom={chrom};start={start};end={end}"
+
+# for species with different format, add the assembly name to the mapping
+# The template should use {chrom}, {start}, and {end} as placeholders.
+ASSEMBLY_TO_API_URL_TEMPLATE = {
+    # Arabidopsis thaliana (TAIR10) - uses hub URL format
+    "TAIR10": "https://api.genome.ucsc.edu/getData/sequence?hubUrl=http://genome.ucsc.edu/goldenPath/help/examples/hubExamples/hubAssembly/plantAraTha1/hub.txt;genome=araTha1;chrom={chrom};start={start};end={end}",
+}
+
+
 # BED element to color mapping (shared between pipeline and app)
 BED_ELEMENT_COLORS = {
     "protein_coding_gene": "#E74C3C",  # Red
@@ -92,9 +106,21 @@ def _sanitize_dna(seq: str) -> str:
 
 
 def _get_dna_sequence(assembly: str, chrom: str, start: int, end: int) -> str:
+    """
+    Fetch DNA sequence from API based on assembly, chromosome, and coordinates.
+    
+    Uses ASSEMBLY_TO_API_URL_TEMPLATE to determine the API URL format for each assembly.
+    Falls back to DEFAULT_API_URL_TEMPLATE if assembly is not in the mapping.
+    """
     if requests is None:
         raise ImportError("requests is required for genome download. Install with: pip install requests")
-    url = f"https://api.genome.ucsc.edu/getData/sequence?genome={assembly};chrom={chrom};start={start};end={end}"
+    
+    # Get API URL template for this assembly, or use default
+    url_template = ASSEMBLY_TO_API_URL_TEMPLATE.get(assembly, DEFAULT_API_URL_TEMPLATE)
+    
+    # Format the URL with the provided parameters
+    url = url_template.format(assembly=assembly, chrom=chrom, start=start, end=end)
+    
     seq = requests.get(url).json()["dna"].upper()
     return seq