add archaea

src/dnaapler/__init__.py

@@ -208,6 +208,7 @@ def chromosome(
 archaea command
 """
 
+
 @main_cli.command()
 @click.help_option("--help", "-h")
 @click.version_option(get_version(), "--version", "-V")
@@ -278,6 +279,7 @@ def archaea(
     # end dnaapler
     end_dnaapler(start_time)
 
+
 """
 Plasmid command
 """
@@ -899,6 +901,8 @@ def all(
         gene = "dnaA,terL"
     elif db == "repa,terl":
         gene = "repA,terL"
+    elif db == "cog1474":
+        gene = "cog1474"
 
     # custom
     if custom_db != "":

src/dnaapler/db/all_db.pjs

@@ -4,12 +4,12 @@
   "dbtype": "Protein",
   "db-version": 5,
   "description": "all.faa",
-  "number-of-letters": 4304128,
-  "number-of-sequences": 8739,
-  "last-updated": "2023-08-15T10:44:00",
+  "number-of-letters": 4463108,
+  "number-of-sequences": 9142,
+  "last-updated": "2024-07-23T22:32:00",
   "number-of-volumes": 1,
-  "bytes-total": 5770444,
-  "bytes-to-cache": 4382868,
+  "bytes-total": 6022224,
+  "bytes-to-cache": 4545475,
   "files": [
     "all_db.pdb",
     "all_db.phr",

src/dnaapler/db/cog1474_db.pjs

@@ -6,10 +6,10 @@
   "description": "cog1474.fasta",
   "number-of-letters": 158980,
   "number-of-sequences": 403,
-  "last-updated": "2024-07-23T15:32:00",
+  "last-updated": "2024-07-23T22:30:00",
   "number-of-volumes": 1,
-  "bytes-total": 272156,
-  "bytes-to-cache": 162704,
+  "bytes-total": 288633,
+  "bytes-to-cache": 162712,
   "files": [
     "cog1474_db.pdb",
     "cog1474_db.phr",

src/dnaapler/utils/all.py

@@ -25,7 +25,7 @@ def all_process_blast_output_and_reorient(
     seed_value: int,
     custom_db: str,
 ) -> None:
-    """Processes the blast output,reorients and saves all contigs into os.path.join(output, f"{prefix}_reoriented.fasta")
+    """Processes the blast output, reorients and saves all contigs into os.path.join(output, f"{prefix}_reoriented.fasta")
 
     :param input: input file
     :param blast_file: blast output file
@@ -174,19 +174,27 @@ def all_process_blast_output_and_reorient(
                 "repA": filtered_df[
                     filtered_df["sseqid"].str.contains("UniRef90", case=False)
                 ].shape[0],
+                "cog1474": filtered_df[
+                    filtered_df["sseqid"].str.contains("cog1474", case=False)
+                ].shape[0],
             }
 
             # if there are hits to more than 1 of dnaA, terL, repA, implement logic
             # to prefer dnaA, repA then terL (in that order)
-            if (counts["dnaA"] > 0) + (counts["terL"] > 0) + (counts["repA"] > 0) >= 2:
+            if (counts["dnaA"] > 0) + (counts["terL"] > 0) + (counts["repA"] > 0) + (counts["cog1474"] > 0)  >= 2:
                 # prefer dnaA if it is greater than zero
                 if counts["dnaA"] > 0:
                     # keep only the hits where dnaA is found
                     filtered_df = filtered_df[
                         filtered_df["sseqid"].str.contains("DNAA")
                     ]
-
-                else:  # where there is repA and terL, keep repA
+                # else prefer cog1474 - archaea if it is greater than zero
+                elif counts["cog1474"] > 0:
+                    filtered_df = filtered_df[
+                        filtered_df["sseqid"].str.contains("cog1474")
+                    ]
+                # otherwise where there is repA and terL, keep repA
+                else:  
                     filtered_df = filtered_df[
                         filtered_df["sseqid"].str.contains("UniRef90")
                     ]
@@ -229,6 +237,9 @@ def all_process_blast_output_and_reorient(
                 # set as dnaA by default
                 gene = "dnaA"
 
+                # for archaea
+                if "cog1474" in filtered_df["sseqid"][0]:
+                    gene = "cog1474"
                 # for plasmids
                 if "UniRef90" in filtered_df["sseqid"][0]:
                     gene = "repA"

src/dnaapler/utils/bulk.py

@@ -57,6 +57,8 @@ def run_bulk_blast(
         db_name = "dnaA_terL_db"
     elif gene == "repA,terL":
         db_name = "repA_terL_db"
+    elif db == "cog1474":
+        gene = "cog1474_db"
 
     # for chromosome, plasmid or phage or all
     # runs blast

tests/test_overall.py

@@ -67,6 +67,17 @@ def test_chrom(tmp_dir):
     cmd = f"dnaapler chromosome -i {input_fasta} -o {tmp_dir} -t 1 -f"
     exec_command(cmd)
 
+def test_all_archaea(tmp_dir):
+    """test all archaea"""
+    input_fasta: Path = f"{overall_test_data}/CP001742.1_archaea.fasta"
+    cmd = f"dnaapler all -i {input_fasta} -o {tmp_dir} -t 1 -f"
+    exec_command(cmd)
+
+def test_archaea(tmp_dir):
+    """test archaea"""
+    input_fasta: Path = f"{overall_test_data}/CP001742.1_archaea.fasta"
+    cmd = f"dnaapler archaea -i {input_fasta} -o {tmp_dir} -t 1 -f"
+    exec_command(cmd)
 
 def test_chrom_start_codon_not_found(tmp_dir):
     """test chrom"""