MAINT: add new files to BuscoDatabaseDirFmt

q2_annotate/busco/database.py

@@ -5,6 +5,7 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
+import os
 import subprocess
 from q2_annotate._utils import colorify, run_command
 from q2_annotate.busco.types import BuscoDatabaseDirFmt
@@ -37,6 +38,9 @@ def fetch_busco_db(
             f"Error during BUSCO database download: {e.returncode}"
         )
 
+    # There is a symlink in the BUSCO database that needs to be removed
+    delete_symlinks(str(busco_db))
+
     # Let user know that the process is complete but it still needs
     # some time to copy files over.
     print(colorify(
@@ -45,3 +49,10 @@ def fetch_busco_db(
     ))
 
     return busco_db
+
+
+def delete_symlinks(root_dir):
+    for dirpath, dirnames, filenames in os.walk(root_dir, followlinks=False):
+        for file in filenames:
+            if os.path.islink(os.path.join(dirpath, file)):
+                os.unlink(os.path.join(dirpath, file))

q2_annotate/busco/tests/test_fetch_busco.py

@@ -5,7 +5,8 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-from q2_annotate.busco.database import fetch_busco_db
+import os
+from q2_annotate.busco.database import fetch_busco_db, delete_symlinks
 from unittest.mock import patch
 from qiime2.plugin.testing import TestPluginBase
 
@@ -36,3 +37,19 @@ def test_fetch_busco_db_all(self, subp_run):
         # Check that command was called in the expected way
         cmd = ["busco", "--download", "all"]
         subp_run.assert_called_once_with(cmd, check=True, cwd=str(busco_db))
+
+    def test_delete_symlinks(self):
+        temp_dir = self.temp_dir.name
+        sub_dir = os.path.join(temp_dir, "subdir")
+        os.makedirs(sub_dir)
+
+        # Create symlinks
+        symlink1 = os.path.join(temp_dir, "symlink1")
+        symlink2 = os.path.join(sub_dir, "symlink2")
+
+        # Run delete function
+        delete_symlinks(temp_dir)
+
+        # Check that symlinks were deleted
+        self.assertFalse(os.path.exists(symlink1))
+        self.assertFalse(os.path.exists(symlink2))

q2_annotate/busco/types/_format.py

@@ -132,6 +132,21 @@ class BuscoDatabaseDirFmt(model.DirectoryFormat):
         r'busco_downloads\/lineages\/.+refseq_db\.faa\.gz',
         format=BuscoGenericBinaryFileFmt
     )
+    information = model.FileCollection(
+        r'busco_downloads\/information\/.+\.txt$',
+        format=BuscoGenericTextFileFmt,
+        optional=True
+    )
+    missing_parasitic = model.File(
+        r'busco_downloads\/lineages\/.+\/missing_in_parasitic\.txt$',
+        format=BuscoGenericTextFileFmt,
+        optional=True
+    )
+    no_hits = model.File(
+        r'busco_downloads\/lineages\/.+\/no_hits$',
+        format=BuscoGenericTextFileFmt,
+        optional=True
+    )
 
     def _path_maker(self, name):
         return str(name)