🐛 Fix GTDB database setup

autometa/taxonomy/gtdb.py

@@ -5,16 +5,15 @@
 File containing definition of the GTDB class and containing functions useful for handling GTDB taxonomy databases
 """
 
+
 import gzip
 import logging
 import os
 import re
-import string
 import tarfile
 import glob
-from pathlib import Path
 
-from typing import Dict, List, Set, Tuple
+from typing import Dict, Set, Tuple
 from itertools import chain
 from tqdm import tqdm
 from typing import Dict
@@ -25,7 +24,6 @@
 from autometa.common.utilities import file_length, is_gz_file
 from autometa.common.external import diamond
 from autometa.taxonomy.database import TaxonomyDatabase
-from autometa.common.exceptions import DatabaseOutOfSyncError
 
 
 logger = logging.getLogger(__name__)
@@ -59,7 +57,9 @@ def create_gtdb_db(reps_faa: str, dbdir: str) -> str:
         reps_faa = dbdir
 
     genome_protein_faa_filepaths = glob.glob(
-        os.path.join(reps_faa, "**", "*_protein.faa"), recursive=True
+        os.path.join(reps_faa, "**", "*_protein.faa*"),
+        recursive=True
+        # To find *_protein.faa and *_protein.faa.gz files
     )
 
     faa_index: Dict[str, str] = {}
@@ -79,12 +79,15 @@ def create_gtdb_db(reps_faa: str, dbdir: str) -> str:
     combined_faa = os.path.join(dbdir, "gtdb.faa")
     with open(combined_faa, "w") as f_out:
         for faa_file, acc in faa_index.items():
-            with open(faa_file) as f_in:
+            with gzip.open(faa_file, "rb") as f_in:
                 for line in f_in:
+                    line = line.decode("utf-8")
                     if line.startswith(">"):
-                        seqheader = line.lstrip(">")
-                        line = f"\n>{acc} {seqheader}"
-                    f_out.write(line)
+                        seqheader = line.lstrip(">").strip()
+                        outline = f">{acc} {seqheader}\n"
+                    else:
+                        outline = line
+                    f_out.write(outline)
     logger.debug(f"Combined GTDB faa file written to {combined_faa}")
     return combined_faa