get-gtdb refactor (#169)

rescript/get_gtdb.py

@@ -10,135 +10,139 @@
 import tempfile
 import tarfile
 import warnings
-
-import qiime2
+import pandas as pd
 from urllib.request import urlretrieve
 from collections import defaultdict
 from urllib.error import HTTPError
-from rescript.get_data import _gzip_decompress
+
+from q2_types.feature_data import (TSVTaxonomyFormat, DNAFASTAFormat,
+ DNAIterator)
 
 # Different versions may have different file names for archaea and
 # 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 = {'214': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
- '207': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
- '202': {'Archaea': 'ar122', 'Bacteria': 'bac120'}}
-
+VERSION_MAP_DICT = {'214.1': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
+ '214.0': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
+ '207.0': {'Archaea': 'ar53', 'Bacteria': 'bac120'},
+ '202.0': {'Archaea': 'ar122', 'Bacteria': 'bac120'}}
 
-def get_gtdb_data(ctx, version='214', domain='Both'):
 
- ver_dom_dict = defaultdict(lambda: defaultdict(dict))
+def get_gtdb_data(
+ version: str = '214.1',
+ domain: str = 'Both',
+ db_type: str = 'SpeciesReps',
+ ) -> (TSVTaxonomyFormat, DNAFASTAFormat):
 
- # Subset dict if needed, but keep same structure
- # Although we can run the following merge actions on a list of one
- # i.e. 'Archaea', we do not want to confuse anyone when looking
- # at provenance, by running a merge command for no reason.
- if domain == 'Both':
- ver_dom_dict[version] = VERSION_MAP_DICT[version]
- else:
- ver_dom_dict[version][domain] = VERSION_MAP_DICT[version][domain]
-
- queries = _assemble_queries(ver_dom_dict)
+ queries = _assemble_queries(version=version,
+ db_type=db_type,
+ domain=domain)
  tax_q, seqs_q = _retrieve_data_from_gtdb(queries)
 
- if domain == 'Both':
- merge_gtdb_seqs = ctx.get_action('feature_table', 'merge_seqs')
- merge_gtdb_taxonomy = ctx.get_action('feature_table', 'merge_taxa')
- print('\n Merging taxonomy data...')
- gtdb_tax, = merge_gtdb_taxonomy(data=tax_q)
- print('\n Merging sequence data...')
- gtdb_seqs, = merge_gtdb_seqs(data=seqs_q)
- else:
- gtdb_tax = tax_q[0]
- gtdb_seqs = seqs_q[0]
-
  print('\n Saving files...\n')
- return gtdb_tax, gtdb_seqs
-
-
-def _assemble_queries(ver_dom_dict):
- queries = defaultdict(lambda: list())
-
- base_seq_url = ('https://data.gtdb.ecogenomic.org/releases/release{ver}/'
- '{ver}.0/genomic_files_reps/{cp}_ssu_reps_r{ver}.tar.gz')
- base_tax_url = ('https://data.gtdb.ecogenomic.org/releases/release{ver}/'
- '{ver}.0/{cp}_taxonomy_r{ver}.tsv.gz')
-
- for version, dcp in ver_dom_dict.items():
- for dom, cp in dcp.items():
-
- queries['Taxonomy'].append(
- (dom,
- base_tax_url.format(**{'ver': version, 'cp': cp}),
- 'FeatureData[Taxonomy]',
- 'HeaderlessTSVTaxonomyFormat'))
-
- queries['Sequence'].append(
- (dom,
- base_seq_url.format(**{'ver': version, 'cp': cp}),
- 'FeatureData[Sequence]',
- 'DNAFASTAFormat'))
+ return tax_q, seqs_q
+
+
+def _assemble_queries(version='214.1',
+ db_type='SpeciesReps',
+ domain='Both'):
+ queries = []
+ base_url = 'https://data.gtdb.ecogenomic.org/releases/'
+ base_version = version.split('.')[0]
+ # ^^ Set `base_version` variable becuase number after the decimal is
+ # only used for the directory. GTDB trims this off for the actual
+ # file names...
+
+ if db_type == 'SpeciesReps':
+ ver_dom_dict = defaultdict(lambda: defaultdict(dict))
+
+ if domain == 'Both':
+ ver_dom_dict[version] = VERSION_MAP_DICT[version]
+ else:
+ ver_dom_dict[version][domain] = VERSION_MAP_DICT[version][domain]
+
+ full_url = (base_url + 'release{bver}/{ver}/genomic_files_reps/'
+ '{cp}_ssu_reps_r{bver}.tar.gz')
+
+ for version, dcp in ver_dom_dict.items():
+ for dom, cp in dcp.items():
+ queries.append((dom,
+ full_url.format(**{'ver': version,
+ 'bver': base_version,
+ 'cp': cp})))
+ elif db_type == 'All':
+ # Note: GTDB does not maintain separate 'Bacteria' and
+ # 'Archaea' files for 'All'. This is only done for
+ # the 'SpeciesReps'.
+ full_url = (base_url + 'release{bver}/{ver}/genomic_files_all/'
+ 'ssu_all_r{bver}.tar.gz')
+
+ queries.append((db_type,
+ full_url.format(**{'ver': version,
+ 'bver': base_version})))
  return queries
 
 
-def _retrieve_data_from_gtdb(queries):
- '''
- Download data from gtdb, given a list of queries.
-
- queries: {'Taxonomy':(domain, url, type, format), (...),
- 'Sequence':(domain, url, type, format), (...)}
- '''
+def parse_gtdb_taxonomy(tax_str):
+ tax = tax_str.split()[0]
+ return tax
 
- tax_results = []
- seq_results = []
-
- print('\nDownloading and processing raw files ... \n')
 
- with tempfile.TemporaryDirectory() as tmpdirname:
- for sttype, q_info in queries.items():
- for domain, url, dtype, fmt in q_info:
- print('Retrieving {0} for {1} from {2}'.format(
- sttype, domain, url))
- # grab url
- bn = os.path.basename(url)
- destination = os.path.join(tmpdirname, bn)
- try:
- urlretrieve(url, destination)
- except HTTPError:
- msg = ("Unable to retrieve the followng file from GTDB:\n "
- + url)
- warnings.warn(msg, UserWarning)
- # seq files are contained within `tar.gz`
- if tarfile.is_tarfile(destination):
- seq_results.append(get_tar_data(destination, bn,
- tmpdirname, dtype, fmt))
- else:
- tax_results.append(get_gzipped_data(destination, bn,
- dtype, fmt))
- return tax_results, seq_results
-
-
-def get_tar_data(tar_loc, base_fn, tmpdirname, dtype, fmt):
+def _get_gtdb_data_path(tmpdirname, url, basename):
+ destination = os.path.join(tmpdirname, basename)
  try:
- untarred_fn = base_fn.split('.')[0]+'.fna'
- print(' Untarring {0}...\n'.format(base_fn))
- with tarfile.open(tar_loc, 'r') as tar:
+ print('Retrieving data from {0}'.format(url))
+ urlretrieve(url, destination)
+ except HTTPError:
+ msg = ("Unable to retrieve the followng file from GTDB:\n "
+ + url)
+ warnings.warn(msg, UserWarning)
+ return destination
+
+
+def _extract_seq_tar_file(tmpdirname, untarred_fn, destination):
+ if tarfile.is_tarfile(destination):
+ with tarfile.open(destination, 'r') as tar:
+ print(' Untarring {0}...\n'.format(untarred_fn))
  tar.extract(member=untarred_fn,
  path=tmpdirname)
- return qiime2.Artifact.import_data(dtype, os.path.join(
-  tmpdirname, untarred_fn), fmt)
- except OSError:
- raise OSError(('{0}: either does not exist or can not '
-  'be untarred!'.format(tar_loc)))
+  # read through gtdb fasta file
+ seqs = DNAFASTAFormat(os.path.join(
+  tmpdirname, untarred_fn),
+  mode="r").view(DNAIterator)
+ return seqs
 
 
-def get_gzipped_data(zipped_loc, base_fn, dtype, fmt):
- try:
- unzipped_destination = os.path.splitext(zipped_loc)[0]
- print(' Unzipping {0}...\n'.format(base_fn))
- _gzip_decompress(zipped_loc, unzipped_destination)
- return qiime2.Artifact.import_data(dtype, unzipped_destination, fmt)
- except OSError:
- raise OSError(('{0}: either does not exist or can not '
- 'be unzipped!'.format(unzipped_destination)))
+def _retrieve_data_from_gtdb(queries):
+ proc_seqs = DNAFASTAFormat()
+ proc_tax = TSVTaxonomyFormat()
+ tax_dict = {}
+
+ print('\nDownloading and processing raw files ... \n')
+ with \
+ tempfile.TemporaryDirectory() as tmpdirname, \
+ proc_seqs.open() as out_fasta, \
+ proc_tax.open() as out_tax:
+
+ for domain, url in queries:
+ # variable setup
+ basename = os.path.basename(url)
+ untarred_fn = basename.split('.')[0]+'.fna'
+ destination = _get_gtdb_data_path(tmpdirname, url, basename)
+ seqs = _extract_seq_tar_file(tmpdirname, untarred_fn, destination)
+ print(' Writing data from \'{0}\'.\n'.format(domain))
+ for seq in seqs:
+ seq.write(out_fasta) # write seq to new fasta file
+ # add taxonomy to dict:
+ tax_dict[seq.metadata['id']] = parse_gtdb_taxonomy(
+ seq.metadata['description'])
+ # set up final taxonomy dataframe:
+ print(' Sequences processed.')
+ print(' Processing taxonomy...')
+ parsed_taxonomy_df = pd.DataFrame.from_dict(tax_dict, orient='index')
+ parsed_taxonomy_df.index.name = 'Feature ID'
+ parsed_taxonomy_df.rename(columns={parsed_taxonomy_df.columns[0]:
+ 'Taxon'}, inplace=True)
+ parsed_taxonomy_df.to_csv(out_tax, sep='\t')
+ print(' Taxonomy processed.')
+ return proc_tax, proc_seqs

rescript/plugin_setup.py

@@ -949,29 +949,39 @@
 )
 
 
-plugin.pipelines.register_function(
+plugin.methods.register_function(
  function=get_gtdb_data,
  inputs={},
  parameters={
- 'version': Str % Choices(['202', '207', '214']),
+ 'version': Str % Choices(['202.0', '207.0', '214.0', '214.1']),
  'domain': Str % Choices(['Both', 'Bacteria', 'Archaea']),
+ 'db_type': Str % Choices(['All', 'SpeciesReps'])
  },
  outputs=[('gtdb_taxonomy', FeatureData[Taxonomy]),
  ('gtdb_sequences', FeatureData[Sequence])],
  input_descriptions={},
  parameter_descriptions={
  'version': 'GTDB database version to download.',
- 'domain': 'Sequence and taxonomy data to download from a given '
+ 'domain': 'SSU sequence and taxonomy data to download from a given '
  'microbial domain from GTDB. \'Both\' will fetch both '
  'bacterial and archaeal data. \'Bacteria\' will only '
  'fetch bacterial data. \'Archaea\' will only fetch '
- 'archaeal data.'},
+ 'archaeal data. This only applies to \'db-type '
+ 'SpeciesReps\'.',
+ 'db_type': '\'All\': All SSU data that pass the quality-control '
+ 'of GTDB, but are not clustered into representative '
+ 'species. \'SpeciesReps\': SSU gene sequences '
+ 'identified within the set of representative '
+ 'species. Note: if \'All\' is used, the \'domain\' '
+ 'parameter will be ignored as GTDB does not maintain '
+ 'separate domain-level files for these non-clustered '
+ 'data.'},
  output_descriptions={
- 'gtdb_taxonomy': 'GTDB reference taxonomy.',
- 'gtdb_sequences': 'GTDB reference sequences.'},
- name='Download, parse, and import GTDB reference data.',
+ 'gtdb_taxonomy': 'SSU GTDB reference taxonomy.',
+ 'gtdb_sequences': 'SSU GTDB reference sequences.'},
+ name='Download, parse, and import SSU GTDB reference data.',
  description=(
- 'Download, parse, and import GTDB files, given a version '
+ 'Download, parse, and import SSU GTDB files, given a version '
  'number. Downloads data directly from GTDB, '
  'parses the taxonomy files, and outputs ready-to-use sequence and '
  'taxonomy artifacts. REQUIRES STABLE INTERNET CONNECTION. ' +

rescript/tests/data/gtdb-seqs.fasta

@@ -0,0 +1,9 @@
+>GB_GCA_000008085.1
+CCCGTTGATCCTGCGGGAGGCCACCGCTATCTCCGTCCGGCTAACCCATGGAAGGCGAGGGTCCCCGGGTAAGGGGGCCCGCCGCACGGCTGAGTAACACGTCGGTAACCTACCCTCGGGACGGGGATAACCCCGGGAAACTGGGGCTAATCCCCGATAGGGGATGGGTGCTGGAAGGCCCCATCCCCGAGAGGGGCTAGCGGTACTTCCCCCGCTAGCCCGCCCGAGGATGGGCCGGCGGCCCATCAGGTAGTTGGCGGGGTAATGGCCCGCCAAGCCGAAGACGGGTAGGGGCCGTGAGAGCGGGAGCCCCCAGATCGGCACTGAGACAAGGGCCGAGGCCCTACGGGGCGCACCAGGGGCGAAACCTCCGCAATGCGGGAAACCGTGACGGGGGGACGGAGAGTGCCGGAGGGCGTTATGCTCTCCGGCTTTTGGGGAGTGTAAGTAGCTCCCCGAATAAGCGGTGGGCAAGAGGGGTGGCAGCCGCCGCGGGAACACCCCCACCGCGAGCGGTGGCCGTGATTATTGGGCCTAAAGGGGCCGTAGCCGGGCCGGTGTGGCTCCGGTGAAATCCTCGGGCTCAACCCGAGGGCGCGCCGGAGCTACTACCGGCCTAGGGACCGGGAGGGGCCGACCGTACTCCCGGGGGAGCGGTGAAATGCTGTAATCCCGGGAGGACGACCCGTGGCGAAAGCGGTCGGCCAGAACGGGTCCGACGGTGAGGGCCGAAGGCCGGGGGCTAGAACGGGATTAGAGACCCCGGTATTCCCGGCTGTCAACGCTGCGGGCTACCTGCTGGGCGGGCTACGAGCCCGCCCAGTGGGGTAGGGAAGCCGTTAAGCCCGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATAGGCGGGGGAGCACACAAGAGGTGGGGTGCGCGGTTTAATTGGATTCGACGCCGGGAACCTCACCGGGGCTGACAGCACAATGATGGTCGGCCTGAAGGGCCTACCGGAGGCGCTGAGAGGAGGTGCATGGCCGCCGTCAGCCTGTGCCGTGAGGTGCCCTGTTAAGTCAGGAAACAGGCGAGACCCGCGCCCGCAGTTGCGACGGCCGAAAGGCCGGCACACTGCGGGGACTGCCGGGGAAACCCGGAGGAAGGTGCGGGCGACGGCAGGTATGCATGCCCCGAATGCCCCGGGCTACACGCGCGCATCAATGGGCGGGACAGGGGGCCGCGACCCCGAAAGGGGGAGCAAATCCCCAAACCCGCTCTCAGTCCAGATCGAGGGCTGCAACTCGCCCTCGTGACGGCGGAATCTCTAGTAGTCGGACGTCACCAGCGTCCGGCGAATACGTCCCTGCTCCTTGCACTCACCGCCCGTCAAGCCACCCGAGCTGGGGCCTAGCGAGGCCGTGGGGGGTTCGCCCCCCACGGTCGAGCTAGGCCCCGGCGAGGGGGGCTAAGTCGACACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCCTA
+>GB_GCA_000016605.1
+TCCGGTTGATCCTGCCGGACCCGATCGCTATAGGGGTAGGGCTAAGCCATGGGAGTCGTACGCTCTCGGGAAGAGGGCGTGGCGGACGGCTGAGTAACACGTGGCTAACCTGCCCTTGGGATCTGGATAACCCCGGGAAACTGGGGCTAATCCGGAGCGGGCAAGGGAATCTGGAATGATCTCTTGCCTAAAAGCCTCTCGGCTGATCCCGTCGAGAGGCGCCCAAGGATGGGGCTGCGGCCCATCAGGCTGTTGGGGGAGTAAAGGTCCCCCAAACCGATAACGGGTAGGGGCCGTGGGAGCGGGAGCCCCCAGTTGGGCACTGAGACAAGGGCCCAGGCCCTACGGGGCGCACCAGGCGCGGAACGTCCCCAATGCGGGAAACCGTGAGGGCGTTACCCCTAGTGCCCTCGCAAGAGGGCTTTTCTCCACTCCAGAAAGGTGGAGGAATAAGCGGGGGGCAAGACTGGTGTCAGCCGCCGCGGTAATACCAGCCCCGCGAGTGATCGGGACGTTTATTGGGCTTAAAGCGCCCGTAGCCGGCCTGTAAAGTCACCGTTTAAAGACCCGGGCTCAACTCGGGGAACGGCGGTGATACTTACAGGCTAGGGGGCGGGAGAGGTCGGAGGTACTCCCGGAGTAGGGGCGAAATCCTCAGATCCCGGGAGGACCACCAGTGGCGAAAGCGTCCGGCTAGAACGCGCCCGACGGTGAGGGGCGAAAGCCGGGGTAGCAAATAGGATTAGATACCCTAGTAGTCCCGGCTGTAAACGATGCAGGCTAGGTGTCGCGTAGGCTTTGTGCCTGCGCGGTGCCGCAGGAAAACTGGTAAGCCCGCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAAGGGGTGGAACCTGCGGCTCAATTGGAGTCAACGCCTGGAATCTCACCGGGGGAGACCGCAGGATGACGGCCAGGCTAACGACCTTGCCAGACTCGCGGAGAGGAGGTGCATGGCCGTCGCCAGCTCGTGTTGTGAAATGTCCGGTTAAGTCCGGCAACGAGCGAGACCCCCACTTCTAGTTGGTAACCGTCTCTCCGGAGACGGTCCACACTAGAAGGACTGCCGGTGTTAAACCGGAGGAAGGAGGGGGCCACGGCAGGTCAGCATGCCCCGAAACTTCCGGGCCGCACGCGGGTTACAATGGCAGGGACAGCGGGATCCGACCCCGAGAGGGGAAGGCAATCCCACAAACCCTGCCTCAGTTGGGATCGAGGGCTGAAACTCGCCCTCGTGAACGAGGAATCCCTAGTAACCGCGGGTCAACAACCCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCGCTCCACCCGAGTGGAGGGGAAGTGAGGCCTCTTGCCCCTCGGGGTGGGAGGTCGAGCTTCTCCTCCGCGAGGGGGGAGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATCACCTCA
+>GB_GCA_000007325.1
+GAAGAGTTTGATCCTGGCTCAGGATGAACGCTGACAGAATGCTTAACACATGCAAGTCTACTTGAATTTGGGTTTTTTAACTTCGATTTGGGTGGCGGACGGGTGAGTAACGCGTAAAGAACTTGCCTCACAGCTAGGGACAACATTTGGAAACGAATGCTAATACCTGATATTATGATTATAGGGCATCCTAGAATTATGAAAGCTATATGCGCTGTGAGAGAGCTTTGCGTCCCATTAGCTAGTTGGAGAGGTAACGGCTCACCAAGGCGATGATGGGTAGCCGGCCTGAGAGGGTGAACGGCCACAAGGGGACTGAGACACGGCCCTTACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGACCGAGAGTCTGATCCAGCAATTCTGTGTGCACGATGACGTTTTTCGGAATGTAAAGTGCTTTCAGTTGGGAAGAAAAAAATGACGGTACCAACAGAAGAAGTGACGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGTCACGAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGTGGTTATGTAAGTCTGATGTGAAAATGCAGGGCTCAACTCTGTATTGCGTTGGAAACTGTGTAACTAGAGTACTGGAGAGGTAAGCGGAACTACAAGTGTAGAGGTGAAATTCGTAGATATTTGTAGGAATGCCGATGGGGAAGCCAGCTTACTGGACAGATACTGACGCTGAAGCGCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGATTACTAGGTGTTGGGGGTCGAACCTCAGCGCCCAAGCAAACGCGATAAGTAATCCGCCTGGGGAGTACGTACGCAAGTATGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAGGAACCTTACCAGCGTTTGACATCTTAGGAATGAGACAGAGATGTTTCAGTGTCCCTTCGGGGAAACCTAAAGACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTTTCGTATGTTACCATCATTAAGTTGGGGACTCATGCGATACTGCCTACGATGAGTAGGAGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATACGCTGGGCTACACACGTGCTACAATGGGTAGAACAGAGAGTTGCAAAGCCGTGAGGTGGAGCTAATCTCAGAAAACTATTCTTAGTTCGGATTGTACTCTGCAACTCGAGTACATGAAGTTGGAATCGCTAGTAATCGCGAATCAGCAATGTCGCGGTGAATACGTTCTCGGGTCTTGTACACACCGCCCGTCACACCACGAGAGTTGGTTGCACCTGAAGTAGCAGGCCTAACCGTAAGGAGGGATGTTCCGAGGGTGTGATTAGCGATTGGGGTGAAGTCGTAACAAGGTATCCGTACGGGAACGTGCGGATGGATCACCTCCTTTC
+>GB_GCA_000008885.1
+GGAGGTGATCCAACCACAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTTATGAACCACAAAGTGGTAAGCGCCCTCCGAAAGGTTAAGCTACCTGCTTCTTTTGCAGCTCACTTCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGCGGCATGCTGATCCGCGATTACTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTAAGACGTACTTTATGAGATTAGCTTACTTTCGCAAGTTTGCTGCCCTTTGTATACGCCATTGTAGCACGTGTGTAGCCCTACTCGTAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCGGTTTATCACCGGCAGTCTCCTTTGAGTTCCCGACTTTTTCGCTGGCAAAAAAGGATAGGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCAGCACCTGTTTTAAAGCTCCCGAAGGCACTAAAGCATCTCTGCTAAATTCTTTAAATGTCAAGAGTAGGTAAGGTTTTTCGCGTTGCATCGAATTAAACCACATGCTCCACCGCTTGTGCGGGCCCCCGTCAATTCATTTGAGTTTTAACCTTGCGATTGTACTCCCCAGGCGGTCGATTTAACGCGTTAGCTTCGAAAACCCCGAGTAAACTCGCAACCTTCAAATCGACATCGTTTACGGCATGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTACATGAGCGTCAGTTTTCGCCCAGGAGGCCGCCTTCGCCGCTGGTATTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCTACCTCCCTCTACGATACTCTAGTTTATTAGTTTCAAATGCAGTTCCTAGGTTGAGCCTAGGGATTTCACATCTGACTTAATAAACCGCCTGCGTACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTCTTCTGCAAGTAACGTCACATAAATATGGTATTATCACATTTACTTTCTTCCCTGCTGAAAGTGCTTTACAATCCGAAGACCTTCTTCACACACGCGGCATAGCTGCATCAGGGTTTCCCCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAGTGTGGCTGGTTATCCTCTCAGACCAGCTAGAGATCGTAGCCTAGGTGAGCATTTACCTCACCTACTAGCTAATCTCATCTGGGTTCATCTAAAAACGCAAGGCTGATATAAAGTATTATATTAGTCCCCTGCTTTGATCTTTCGATATTATGCGGTATTAGCTACCGTTTCCAGTAGTTGTCCCCCTTTTTTAGGCAGATCCCCAGACATTACTCACCCGTTCGCCGCTCGCCGTCAAAGAAAAATCTCTACGCTGCCGCACGACTTGCATGTGTTAGGCTTGCCGCTAGCGTTCAATCTGAGCCATGATCAAACTCTTCAAT
+

rescript/tests/data/gtdb-tax.tsv

@@ -0,0 +1,6 @@
+Feature ID Taxon
+GB_GCA_000008085.1 d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__Nanoarchaeales;f__Nanoarchaeaceae;g__Nanoarchaeum;s__Nanoarchaeum equitans
+GB_GCA_000016605.1 d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Metallosphaera;s__Metallosphaera sedula
+GB_GCA_000007325.1 d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium;s__Fusobacterium nucleatum
+GB_GCA_000008885.1 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Wigglesworthia;s__Wigglesworthia glossinidia_A
+