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added GTDB v232 as available download option #254

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Merged
mikerobeson merged 1 commit into from
May 4, 2026
Merged

added GTDB v232 as available download option #254

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9 changes: 5 additions & 4 deletions rescript/get_gtdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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'},
Expand All @@ -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'
Expand All @@ -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'):
Expand All @@ -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'
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2 changes: 1 addition & 1 deletion rescript/plugin_setup.py
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Expand Up @@ -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'])
Expand Down
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