Merge pull request #81 from gbouras13/dev

v0.8.1

.github/workflows/ci.yaml

@@ -49,6 +49,6 @@ jobs:
         shell: bash -l {0}
         run: just test-ci
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
 
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dnaapler"
-version = "0.8.0" # change VERSION too
+version = "0.8.1" # change VERSION too
 description = "Reorients assembled microbial sequences"
 authors = ["George Bouras <[email protected]>"]
 license = "MIT"

src/dnaapler/__init__.py

@@ -905,6 +905,18 @@ def all(
         gene = "repA,terL"
     elif db == "cog1474":
         gene = "cog1474"
+    elif db == "dnaA,cog1474":
+        gene = "dnaA,cog1474"
+    elif db == "cog1474,terl":
+        gene = "cog1474,terL"
+    elif db == "repa,cog1474":
+        gene = "repA,cog1474"
+    elif db == "dnaa,repa,cog1474":
+        gene = "dnaa,repa,cog1474"
+    elif db == "dnaa,terl,cog1474":
+        gene = "dnaa,terl,cog1474"
+    elif db == "repa,terl,cog1474":
+        gene = "repa,terl,cog1474"
 
     # custom
     if custom_db != "":

src/dnaapler/utils/VERSION

@@ -1 +1 @@
-0.8.0
+0.8.1

src/dnaapler/utils/validation.py

@@ -218,7 +218,22 @@ def validate_choice_db(ctx, param, value):
     """
     checks the click.Choice option for the mode flag in bulk subcommand
     """
-    choices = ["all", "dnaa", "repa", "terl", "dnaa,repa", "dnaa,terl", "repa,terl"]
+    choices = [
+        "all",
+        "dnaa",
+        "repa",
+        "terl",
+        "dnaa,repa",
+        "dnaa,terl",
+        "repa,terl",
+        "cog1474",
+        "dnaA,cog1474",
+        "cog1474,terl",
+        "repa,cog1474",
+        "dnaa,repa,cog1474",
+        "dnaa,terl,cog1474",
+        "repa,terl,cog1474",
+    ]
     if value not in choices:
         raise click.BadParameter(f"Invalid choice. Choose from {', '.join(choices)}")
     return value

tests/test_overall.py

@@ -246,6 +246,18 @@ def test_all_dnaa_repa(tmp_dir):
     exec_command(cmd)
 
 
+"""
+this one is for hybracter
+"""
+
+
+def test_all_dnaa_repa_cog1474(tmp_dir):
+    """test all dnaa repa cog1474 - for hybracter"""
+    input_fasta: Path = f"{overall_test_data}/all_test.fasta"
+    cmd = f"dnaapler all  -i {input_fasta} -o {tmp_dir} -t 1 -f --db dnaa,repa,cog1474"
+    exec_command(cmd)
+
+
 def test_all_dnaa_terl(tmp_dir):
     """test all dnaa terl"""
     input_fasta: Path = f"{overall_test_data}/all_reorient_and_no_reorient.fasta"