Merge pull request #177 from r2dt-bio/tmrna-tweaks

Tmrna tweaks
r2dt-bio · Feb 2, 2025 · 2d864c4 · 2d864c4
2 parents 9b42680 + 8ecb57f
commit 2d864c4
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Showing 2 changed files with 12 additions and 1 deletion.
diff --git a/data/tmrna/metadata.tsv b/data/tmrna/metadata.tsv
@@ -0,0 +1,7 @@
+model_name	species	taxid	rna_type
+tmRNA	Bacteria	2	tmRNA
+tmRNA_alpha	Alphaproteobacteria	28211	tmRNA
+tmRNA_beta	Betaproteobacteria	28216	tmRNA
+tmRNA_cyano	Cyanobacteriota	1117	tmRNA
+tmRNA_intron	bacteria	2	tmRNA
+tmRNA_mito	Eukaryota	2759	tmRNA
diff --git a/utils/list_models.py b/utils/list_models.py
@@ -160,6 +160,8 @@ def get_models(source, modelinfo_file, metadata_file):
         rna_type = "large subunit rRNA"
     elif source == "RNAse P Database":
         rna_type = "RNAse P"
+    elif source == "tmRNA Database":
+        rna_type = "tmRNA"
     else:
         rna_type = ""
     for model_id in model_ids:
@@ -255,14 +257,16 @@ def list_models():
         os.path.join(config.RNASEP_CM_LIBRARY, "modelinfo.txt"),
         os.path.join(config.RNASEP, "metadata.tsv"),
     )
+    data = data + models
+    print(f"RNAse P Database: {len(models)}")
 
     models = get_models(
         "tmRNA Database",
         os.path.join(config.TMRNA_CM_LIBRARY, "modelinfo.txt"),
         os.path.join(config.TMRNA, "metadata.tsv"),
     )
     data = data + models
-    print(f"RNAse P Database: {len(models)}")
+    print(f"tmRNA Database: {len(models)}")
 
     models = get_rfam_models()
     data = data + models