a few fixes

CHANGELOG.md

@@ -1,6 +1,12 @@
 
 # Changelog
 
+## v0.3.1 rpetit3/camlhmp "Maybe a cat?" 2024/08/05
+
+### `Fixed`
+
+- `camlhmp-blast-alleles` not having a default value for targets
+
 ## v0.3.0 rpetit3/camlhmp "More bunnies and fewer baby birds" 2024/08/05
 
 ### `Added`

camlhmp/parsers/blast.py

@@ -49,6 +49,15 @@ def get_blast_allele_hits(
                 })
 
     final_allele_hits = {}
+    for target in targets:
+        final_allele_hits[target] = {
+            "id": "-",
+            "qcovs": 0,
+            "pident": 0,
+            "bitscore": 0,
+            "comment": "No hits met thresholds",
+        }
+
     for target in target_results:
         if len(target_results[target]["known"]):
             # exact matches to known alleles were found
@@ -75,15 +84,6 @@ def get_blast_allele_hits(
                 # multiple hits, only report highest score
                 final_allele_hits[target] = sorted(target_results[target]["novel"], key=lambda x: x["bitscore"], reverse=True)[0]
                 final_allele_hits[target]["comment"] = "No exact matches to known alleles"
-        else:
-            # no hits
-            final_allele_hits[target] = {
-                "id": "-",
-                "qcovs": 0,
-                "pident": 0,
-                "bitscore": 0,
-                "comment": "No hits met thresholds",
-            }
 
     # Debugging information
     logging.debug("camlhmp.engines.blast.get_blast_allele_hits")

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "camlhmp"
-version = "0.3.0"
+version = "0.3.1"
 description = "Classification through yAML Heuristic Mapping Protocol"
 authors = [
     "Robert A. Petit III <[email protected]>",

tests/data/blast/alleles/spn-pbptype.yaml

@@ -12,13 +12,14 @@ metadata:
 engine:
   type: blast   # The type of tool used to generate the data
   tool: tblastn # The tool used to generate the data
+
 # targets provides a list of sequence targets (primers, genes, proteins, etc...)
-targets: ["1A", "2A", "2X"]
+targets: ["1A", "2B", "2X"]
 # types includes the final typing designations based on targets and aliases 
 types:
   - name: "1A"           # name of the profile
     targets: ["1A"]      # list of targets that are part of the profile
-  - name: "2A"
-    targets: ["2A"]
+  - name: "2B"
+    targets: ["2B"]
   - name: "2X"
     targets: ["2X"]