added GTDB v232 as available download option (bokulich-lab#254)

No need for code review.. just added the new DB, ran the test code. All passed.

Author: mikerobeson

rescript/get_gtdb.py

@@ -24,7 +24,8 @@
 # bacteria. for example 'ar53' and 'bac120' mean that the GTDB phylogeny
 # is based on 53 and 120 concatenated proteins (cp), respectively.
 # If this changes we can set up a conditional statemnt below.
-VERSION_MAP_DICT = {'226.0': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
+VERSION_MAP_DICT = {'232.0': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
+                    '226.0': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
                     '220.0': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
                     '214.1': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
                     '214.0': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
@@ -33,7 +34,7 @@
 
 
 def get_gtdb_data(
-    version: str = '226.0',
+    version: str = '232.0',
     domain: str = 'Both',
     db_type: str = 'SpeciesReps',
     url_type: str = 'Primary'
@@ -49,7 +50,7 @@ def get_gtdb_data(
     return tax_q, seqs_q
 
 
-def _assemble_queries(version='226.0',
+def _assemble_queries(version='232.0',
                       db_type='SpeciesReps',
                       domain='Both',
                       url_type='Primary'):
@@ -66,7 +67,7 @@ def _assemble_queries(version='226.0',
     # file names...
     # GTDB v220 started storing the ssu_reps FASTA files
     # as 'fna.gz' instead of their usual 'tar.gz'.
-    if version in ['220.0', '226.0']:
+    if version in ['220.0', '226.0', '232.0']:
         stype = 'fna'
     else:
         stype = 'tar'

rescript/plugin_setup.py

@@ -912,7 +912,7 @@
     inputs={},
     parameters={
         'version': Str % Choices(['202.0', '207.0', '214.0', '214.1',
-                                  '220.0', '226.0']),
+                                  '220.0', '226.0', '232.0']),
         'domain': Str % Choices(['Both', 'Bacteria', 'Archaea']),
         'db_type': Str % Choices(['All', 'SpeciesReps']),
         'url_type': Str % Choices(['Primary', 'Mirror'])