From 73042f7fec14b51eda671da60c390436511a7518 Mon Sep 17 00:00:00 2001
From: gbouras13 <george.bouras@adelaide.edu.au>
Date: Mon, 16 Sep 2024 13:05:53 +0930
Subject: [PATCH] add dnaa,repa,cog1474 option for hybracter

---
 pyproject.toml                   |  2 +-
 src/dnaapler/__init__.py         | 12 ++++++++++++
 src/dnaapler/utils/VERSION       |  2 +-
 src/dnaapler/utils/validation.py |  2 +-
 tests/test_overall.py            |  9 +++++++++
 5 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 66abbed..2ff2e20 100644
--- a/pyproject.toml
+++ b/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 <george.bouras@adelaide.edu.au>"]
 license = "MIT"
diff --git a/src/dnaapler/__init__.py b/src/dnaapler/__init__.py
index 7de1f4c..ef60096 100755
--- a/src/dnaapler/__init__.py
+++ b/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 != "":
diff --git a/src/dnaapler/utils/VERSION b/src/dnaapler/utils/VERSION
index 8adc70f..c18d72b 100644
--- a/src/dnaapler/utils/VERSION
+++ b/src/dnaapler/utils/VERSION
@@ -1 +1 @@
-0.8.0
\ No newline at end of file
+0.8.1
\ No newline at end of file
diff --git a/src/dnaapler/utils/validation.py b/src/dnaapler/utils/validation.py
index f221f8b..e6ab45a 100644
--- a/src/dnaapler/utils/validation.py
+++ b/src/dnaapler/utils/validation.py
@@ -218,7 +218,7 @@ 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
diff --git a/tests/test_overall.py b/tests/test_overall.py
index 1b74e4a..9e0d015 100755
--- a/tests/test_overall.py
+++ b/tests/test_overall.py
@@ -245,6 +245,15 @@ def test_all_dnaa_repa(tmp_dir):
     cmd = f"dnaapler all  -i {input_fasta} -o {tmp_dir} -t 1 -f --db dnaa,repa"
     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"""