diff --git a/rescript/get_gtdb.py b/rescript/get_gtdb.py index 0c98e54..d74a7e3 100644 --- a/rescript/get_gtdb.py +++ b/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' diff --git a/rescript/plugin_setup.py b/rescript/plugin_setup.py index e772bf8..51b7f98 100644 --- a/rescript/plugin_setup.py +++ b/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'])