def run(self,
prev_gtdb_metadata_file,
cur_gtdb_metadata_file,
cur_uba_gid_file,
genomes_new_updated_file,
qc_passed_file,
gtdbtk_classify_file,
ncbi_genbank_assembly_file,
untrustworthy_type_file,
gtdb_type_strains_ledger):
"""Identify species representatives that have changed from previous release."""
# create previous and current GTDB genome sets
self.logger.info('Creating previous GTDB genome set.')
prev_genomes = Genomes()
prev_genomes.load_from_metadata_file(prev_gtdb_metadata_file,
gtdb_type_strains_ledger=gtdb_type_strains_ledger,
uba_genome_file=cur_uba_gid_file,
ncbi_genbank_assembly_file=ncbi_genbank_assembly_file,
untrustworthy_type_ledger=untrustworthy_type_file)
self.logger.info(f' ...previous genome set contains {len(prev_genomes):,} genomes.')
self.logger.info(' ...previous genome set has {:,} species clusters spanning {:,} genomes.'.format(
len(prev_genomes.sp_clusters),
prev_genomes.sp_clusters.total_num_genomes()))
self.logger.info('Creating current GTDB genome set.')
cur_genomes = Genomes()
cur_genomes.load_from_metadata_file(cur_gtdb_metadata_file,
gtdb_type_strains_ledger=gtdb_type_strains_ledger,
create_sp_clusters=False,
uba_genome_file=cur_uba_gid_file,
qc_passed_file=qc_passed_file,
ncbi_genbank_assembly_file=ncbi_genbank_assembly_file,
untrustworthy_type_ledger=untrustworthy_type_file)
self.logger.info(f' ...current genome set contains {len(cur_genomes):,} genomes.')
# get previous and current genomes from type strains
self.logger.info('Determining genomes identified as being assembled from type strain.')
prev_type_strain_gids = prev_genomes.gtdb_type_strain_genomes()
cur_type_strain_gids = cur_genomes.gtdb_type_strain_genomes()
new_type_strain_gids = cur_type_strain_gids - prev_type_strain_gids
self.logger.info(' ...identified {:,} previous and {:,} current genomes from type strain.'.format(
len(prev_type_strain_gids),
len(cur_type_strain_gids)))
self.logger.info(' ...{:,} type strain genomes are new to the current genome set.'.format(
len(new_type_strain_gids)))
# created expanded previous GTDB species clusters
self.logger.info('Creating species clusters of new and updated genomes based on GTDB-Tk classifications.')
new_updated_sp_clusters = SpeciesClusters()
new_updated_sp_clusters.create_expanded_clusters(prev_genomes.sp_clusters,
genomes_new_updated_file,
qc_passed_file,
gtdbtk_classify_file)
self.logger.info('Identified {:,} expanded species clusters spanning {:,} genomes.'.format(
len(new_updated_sp_clusters),
new_updated_sp_clusters.total_num_genomes()))
# determine status of each previous GTDB representative
self.logger.info('Determining status of each previous GTDB representative.')
fout_summary = open(os.path.join(self.output_dir, 'rep_change_summary.tsv'), 'w')
fout_summary.write('Genome ID\tPrevious GTDB species\tNo. genomes in cluster')
fout_summary.write('\tGENOMIC_CHANGE\tNCBI_SPECIES_CHANGE\tTYPE_STRAIN_CHANGE\tDOMAIN_CHECK')
fout_summary.write('\tNew type strains\tRepresentative changed\n')
fout_detailed = open(os.path.join(self.output_dir, 'rep_change_detailed.tsv'), 'w')
fout_detailed.write('Genome ID\tPrevious GTDB species\tChange type\tChange\n')
unchanged_genome = set()
updated_genome = set()
lost_genome = set()
user_genome = set()
unchanged_sp = set()
reassigned_sp = set()
unchanged_type_strain = set()
lost_type_strain = set()
gain_type_strain = set()
new_type_strain = set()
changed_domain = set()
unchanged_domain = set()
num_rep_changes = 0
first_type_strain = set()
for prev_rid, prev_gtdb_sp in prev_genomes.sp_clusters.species():
fout_summary.write(f'{prev_rid}\t{prev_gtdb_sp}\t{len(prev_genomes.sp_clusters[prev_rid])}')
if prev_rid in cur_genomes:
# check if genome assembly has been updated
if prev_rid in new_updated_sp_clusters.updated_gids:
updated_genome.add(prev_rid)
fout_summary.write('\tUPDATED')
prev_ncbi_accn = prev_genomes[prev_rid].ncbi_accn
cur_ncbi_accn = cur_genomes[prev_rid].ncbi_accn
assert(prev_ncbi_accn != cur_ncbi_accn)
fout_detailed.write((f'{prev_rid}\t{prev_gtdb_sp}\tGENOMIC_CHANGE:UPDATED\tNCBI accession updated from '
f'{prev_genomes[prev_rid].ncbi_accn} to {cur_genomes[prev_rid].ncbi_accn}\n'))
else:
unchanged_genome.add(prev_rid)
fout_summary.write('\tUNCHANGED')
# check if NCBI species assignment has changed
prev_ncbi_sp = prev_genomes[prev_rid].ncbi_taxa.species
cur_ncbi_sp = cur_genomes[prev_rid].ncbi_taxa.species
if prev_genomes[prev_rid].ncbi_taxa.specific_epithet == cur_genomes[prev_rid].ncbi_taxa.specific_epithet:
unchanged_sp.add(prev_rid)
fout_summary.write('\tUNCHANGED')
else:
reassigned_sp.add(prev_rid)
fout_summary.write('\tREASSIGNED')
fout_detailed.write(f'{prev_rid}\t{prev_gtdb_sp}\tNCBI_SPECIES_CHANGE:REASSIGNED\tNCBI species reassigned from {prev_ncbi_sp} to {cur_ncbi_sp}\n')
# check if type material status has changed
if prev_rid in prev_type_strain_gids and prev_rid in cur_type_strain_gids:
unchanged_type_strain.add(prev_rid)
fout_summary.write('\tUNCHANGED')
elif prev_rid not in prev_type_strain_gids and prev_rid not in cur_type_strain_gids:
unchanged_type_strain.add(prev_rid)
fout_summary.write('\tUNCHANGED')
elif prev_rid in prev_type_strain_gids and prev_rid not in cur_type_strain_gids:
lost_type_strain.add(prev_rid)
fout_summary.write('\tLOST')
fout_detailed.write(f'{prev_rid}\t{prev_gtdb_sp}\tTYPE_STRAIN_CHANGE:LOST\tNo longer considered a genome from type strain\n')
elif prev_rid not in prev_type_strain_gids and prev_rid in cur_type_strain_gids:
gain_type_strain.add(prev_rid)
fout_summary.write('\tGAINED')
fout_detailed.write(f'{prev_rid}\t{prev_gtdb_sp}\tTYPE_STRAIN_CHANGE:GAINED\tNow considered a genome from type strain\n')
else:
assert(False)
# check if domain assignment has changed
if prev_genomes[prev_rid].gtdb_taxa.domain != cur_genomes[prev_rid].gtdb_taxa.domain:
changed_domain.add(prev_rid)
fout_detailed.write('{}\t{}\tDOMAIN_CHECK:REASSIGNED\tRepresentative changed from {} to {}\n'.format(
prev_rid,
prev_gtdb_sp,
prev_genomes[prev_rid].gtdb_taxa.domain,
cur_genomes[prev_rid].gtdb_taxa.domain))
fout_summary.write('\tREASSIGNED')
else:
unchanged_domain.add(prev_rid)
fout_summary.write('\tUNCHANGED')
# check if genome cluster has new genomes assembled from the type strain of the species
sp_gids = prev_genomes.sp_clusters[prev_rid]
if prev_rid in new_updated_sp_clusters:
sp_gids = sp_gids.union(new_updated_sp_clusters[prev_rid])
new_ts = new_type_strain_gids.intersection(sp_gids)
if new_ts:
if not prev_type_strain_gids.intersection(sp_gids) and not new_ts.intersection(gain_type_strain):
first_type_strain.add(prev_gtdb_sp)
new_type_strain.add(prev_rid)
fout_detailed.write('{}\t{}\tNEW_TYPE_STRAINS:NEW\tSpecies cluster has {:,} new genomes from type strain: {}\n'.format(
prev_rid,
prev_gtdb_sp,
len(new_ts),
','.join(new_ts)))
fout_summary.write(f'\t{len(new_ts)}')
if (prev_rid in unchanged_genome
and prev_rid in unchanged_sp
and prev_rid in unchanged_type_strain
and prev_rid in unchanged_domain):
fout_summary.write('\tNO')
else:
fout_summary.write('\tYES')
num_rep_changes += 1
fout_summary.write('\n')
else:
lost_genome.add(prev_rid)
fout_summary.write('\t{}\t{}\t{}\t{}\t{}\n'.format('LOST','N/A','N/A','N/A', 'YES'))
fout_detailed.write(f'{prev_rid}\t{prev_gtdb_sp}\tGENOMIC_CHANGE:LOST\tGenome not present in current GTDB release\n')
num_rep_changes += 1
fout_summary.close()
fout_detailed.close()
num_prev_sp_clusters = len(prev_genomes.sp_clusters)
num_rep_changes_perc = num_rep_changes*100.0/num_prev_sp_clusters
self.logger.info(f' ... identified {num_rep_changes:,} ({num_rep_changes_perc:.1f}%) species with a change to the representative genome.')
self.logger.info('Genomic changes:')
unchanged_perc = len(unchanged_genome)*100.0 / num_prev_sp_clusters
updated_perc = len(updated_genome)*100.0 / num_prev_sp_clusters
lost_perc = len(lost_genome)*100.0 / num_prev_sp_clusters
user_perc = len(user_genome)*100.0 / num_prev_sp_clusters
self.logger.info(f' unchanged_genome: {len(unchanged_genome):,} ({unchanged_perc:.1f}%)')
self.logger.info(f' updated_genome: {len(updated_genome):,} ({updated_perc:.1f}%)')
self.logger.info(f' lost_genome: {len(lost_genome):,} ({lost_perc:.1f}%)')
self.logger.info(f' user_genome: {len(user_genome):,} ({user_perc:.1f}%)')
self.logger.info('NCBI species assignment changes:')
cur_sp_count = len(unchanged_genome) + len(updated_genome)
unchanged_sp_perc = len(unchanged_sp)*100.0 / cur_sp_count
reassigned_sp_perc = len(reassigned_sp)*100.0 / cur_sp_count
self.logger.info(f' unchanged_sp: {len(unchanged_sp):,} ({unchanged_sp_perc:.1f}%)')
self.logger.info(f' reassigned_sp: {len(reassigned_sp):,} ({reassigned_sp_perc:.1f}%)')
self.logger.info('Status of type strain genome declarations:')
prev_ts_count = len(unchanged_type_strain) + len(lost_type_strain)
unchanged_type_strain_perc = len(unchanged_type_strain)*100.0 / prev_ts_count
lost_type_strain_perc = len(lost_type_strain)*100.0 / prev_ts_count
gain_type_strain_perc = len(gain_type_strain)*100.0 / prev_ts_count
new_type_strain_perc = len(new_type_strain)*100.0 / prev_ts_count
self.logger.info(f' unchanged_type_strain: {len(unchanged_type_strain):,} ({unchanged_type_strain_perc:.1f}%)')
self.logger.info(f' lost_type_strain: {len(lost_type_strain):,} ({lost_type_strain_perc:.1f}%)')
self.logger.info(f' gain_type_strain: {len(gain_type_strain):,} ({gain_type_strain_perc:.1f}%)')
self.logger.info(f' new_type_strain: {len(new_type_strain):,} ({new_type_strain_perc:.1f}%)')
self.logger.info('GTDB domain assignment change:')
unchanged_domain_perc = len(unchanged_domain)*100.0 / num_prev_sp_clusters
changed_domain_perc = len(changed_domain)*100.0 / num_prev_sp_clusters
self.logger.info(f' unchanged: {len(unchanged_domain):,} ({unchanged_domain_perc:.1f}%)')
self.logger.info(f' reassigned: {len(changed_domain):,} ({changed_domain_perc:.1f}%)')
print('first_type_strain', len(first_type_strain))
def run(self, prev_gtdb_metadata_file, cur_gtdb_metadata_file,
genomes_new_updated_file, qc_passed_file, gtdbtk_classify_file,
ncbi_genbank_assembly_file, untrustworthy_type_file,
disband_cluster_ledger, gtdb_type_strains_ledger,
ncbi_env_bioproject_ledger):
"""Identify species representatives that have changed from previous release."""
# create previous and current GTDB genome sets
self.logger.info('Creating previous GTDB genome set.')
prev_genomes = Genomes()
prev_genomes.load_from_metadata_file(
prev_gtdb_metadata_file,
gtdb_type_strains_ledger=gtdb_type_strains_ledger,
ncbi_genbank_assembly_file=ncbi_genbank_assembly_file,
untrustworthy_type_ledger=untrustworthy_type_file,
ncbi_env_bioproject_ledger=ncbi_env_bioproject_ledger)
self.logger.info(
f' - previous genome set contains {len(prev_genomes):,} genomes.')
self.logger.info(
' - previous genome set has {:,} species clusters spanning {:,} genomes.'
.format(len(prev_genomes.sp_clusters),
prev_genomes.sp_clusters.total_num_genomes()))
self.logger.info('Creating current GTDB genome set.')
cur_genomes = Genomes()
cur_genomes.load_from_metadata_file(
cur_gtdb_metadata_file,
gtdb_type_strains_ledger=gtdb_type_strains_ledger,
create_sp_clusters=False,
qc_passed_file=qc_passed_file,
ncbi_genbank_assembly_file=ncbi_genbank_assembly_file,
untrustworthy_type_ledger=untrustworthy_type_file,
ncbi_env_bioproject_ledger=ncbi_env_bioproject_ledger)
# get previous and current genomes from type strains
self.logger.info(
'Determining genomes identified as being assembled from type strain.'
)
prev_type_strain_gids = prev_genomes.gtdb_type_strain_genomes()
cur_type_strain_gids = cur_genomes.gtdb_type_strain_genomes()
new_type_strain_gids = cur_type_strain_gids - prev_type_strain_gids
self.logger.info(
' - identified {:,} previous and {:,} current genomes from type strain.'
.format(len(prev_type_strain_gids), len(cur_type_strain_gids)))
self.logger.info(
' - {:,} type strain genomes are new to the current genome set.'.
format(len(new_type_strain_gids)))
# create expanded previous GTDB species clusters
self.logger.info(
'Creating species clusters of new and updated genomes based on GTDB-Tk classifications.'
)
new_updated_sp_clusters = SpeciesClusters()
new_updated_sp_clusters.create_expanded_clusters(
prev_genomes, genomes_new_updated_file, qc_passed_file,
gtdbtk_classify_file)
self.logger.info(
'Identified {:,} expanded species clusters spanning {:,} genomes.'.
format(len(new_updated_sp_clusters),
new_updated_sp_clusters.total_num_genomes()))
# read GTDB clusters to be disbanded
self.logger.info(
'Parsing ledger indicating GTDB clusters to be disbanded.')
disbanded_rids = parse_disbanded_cluster_ledger(disband_cluster_ledger)
self.logger.info(' - identified {:,} clusters to be disbanded.'.format(
len(disbanded_rids)))
# determine status of each previous GTDB representative
self.logger.info(
'Determining status of each previous GTDB representative.')
fout_summary = open(
os.path.join(self.output_dir, 'rep_change_summary.tsv'), 'w')
fout_summary.write(
'Genome ID\tPrevious GTDB species\tNo. genomes in cluster')
fout_summary.write(
'\tGENOMIC_CHANGE\tNCBI_SPECIES_CHANGE\tTYPE_STRAIN_CHANGE\tDOMAIN_CHECK\tNCBI_ASSEMBLY_QUALITY\tDISBANDED_CHECK'
)
fout_summary.write('\tNew type strains\tRepresentative changed\n')
fout_detailed = open(
os.path.join(self.output_dir, 'rep_change_detailed.tsv'), 'w')
fout_detailed.write(
'Genome ID\tPrevious GTDB species\tChange type\tChange\n')
unchanged_genome = set()
updated_genome = set()
lost_genome = set()
unchanged_sp = set()
reassigned_sp = set()
unchanged_type_strain = set()
lost_type_strain = set()
gain_type_strain = set()
new_type_strain = set()
ncbi_anomalous_assembly = set()
changed_domain = set()
unchanged_domain = set()
num_rep_changes = 0
disbanded_count = 0
for prev_rid, prev_gtdb_sp in prev_genomes.sp_clusters.species():
fout_summary.write(
f'{prev_rid}\t{prev_gtdb_sp}\t{len(prev_genomes.sp_clusters[prev_rid])}'
)
if prev_rid in cur_genomes:
# check if genome assembly has been updated
if prev_rid in new_updated_sp_clusters.updated_gids:
updated_genome.add(prev_rid)
fout_summary.write('\tUPDATED')
prev_ncbi_accn = prev_genomes[prev_rid].ncbi_accn
cur_ncbi_accn = cur_genomes[prev_rid].ncbi_accn
assert prev_ncbi_accn != cur_ncbi_accn
fout_detailed.write((
f'{prev_rid}\t{prev_gtdb_sp}\tGENOMIC_CHANGE:UPDATED\tNCBI accession updated from '
f'{prev_genomes[prev_rid].ncbi_accn} to {cur_genomes[prev_rid].ncbi_accn}\n'
))
else:
unchanged_genome.add(prev_rid)
fout_summary.write('\tUNCHANGED')
# check if NCBI species assignment has changed
prev_ncbi_sp = prev_genomes[prev_rid].ncbi_taxa.species
cur_ncbi_sp = cur_genomes[prev_rid].ncbi_taxa.species
if prev_genomes[
prev_rid].ncbi_taxa.specific_epithet == cur_genomes[
prev_rid].ncbi_taxa.specific_epithet:
unchanged_sp.add(prev_rid)
fout_summary.write('\tUNCHANGED')
else:
reassigned_sp.add(prev_rid)
fout_summary.write('\tREASSIGNED')
fout_detailed.write(
f'{prev_rid}\t{prev_gtdb_sp}\tNCBI_SPECIES_CHANGE:REASSIGNED\tNCBI species reassigned from {prev_ncbi_sp} to {cur_ncbi_sp}\n'
)
# check if type material status has changed
if prev_rid in prev_type_strain_gids and prev_rid in cur_type_strain_gids:
unchanged_type_strain.add(prev_rid)
fout_summary.write('\tUNCHANGED')
elif prev_rid not in prev_type_strain_gids and prev_rid not in cur_type_strain_gids:
unchanged_type_strain.add(prev_rid)
fout_summary.write('\tUNCHANGED')
elif prev_rid in prev_type_strain_gids and prev_rid not in cur_type_strain_gids:
lost_type_strain.add(prev_rid)
fout_summary.write('\tLOST')
fout_detailed.write(
f'{prev_rid}\t{prev_gtdb_sp}\tTYPE_STRAIN_CHANGE:LOST\tNo longer considered a genome from type strain\n'
)
elif prev_rid not in prev_type_strain_gids and prev_rid in cur_type_strain_gids:
gain_type_strain.add(prev_rid)
fout_summary.write('\tGAINED')
fout_detailed.write(
f'{prev_rid}\t{prev_gtdb_sp}\tTYPE_STRAIN_CHANGE:GAINED\tNow considered a genome from type strain\n'
)
else:
assert False
# check if domain assignment has changed
if prev_genomes[prev_rid].gtdb_taxa.domain != cur_genomes[
prev_rid].gtdb_taxa.domain:
changed_domain.add(prev_rid)
fout_detailed.write(
'{}\t{}\tDOMAIN_CHECK:REASSIGNED\tRepresentative changed from {} to {}\n'
.format(prev_rid, prev_gtdb_sp,
prev_genomes[prev_rid].gtdb_taxa.domain,
cur_genomes[prev_rid].gtdb_taxa.domain))
fout_summary.write('\tREASSIGNED')
else:
unchanged_domain.add(prev_rid)
fout_summary.write('\tUNCHANGED')
# check if NCBI has marked genome assembly as problematic
if cur_genomes[prev_rid].is_ncbi_many_frameshifted_proteins(
) or cur_genomes[prev_rid].is_ncbi_anomalous_assembly():
ncbi_anomalous_assembly.add(prev_rid)
fout_summary.write('\tNCBI_ANOMALOUS_ASSEMBLY')
fout_detailed.write(
'{}\t{}\tNCBI_ASSEMBLY_METADATA:NCBI_ANOMALOUS_ASSEMBLY\tExcluded = {}\n'
.format(
prev_rid, prev_gtdb_sp,
cur_genomes[prev_rid].excluded_from_refseq_note))
else:
fout_summary.write('\tNCBI_GOOD_ASSEMBLY')
# check if GTDB species cluster is flagged to be disbanded
if prev_rid in disbanded_rids:
disbanded_count += 1
fout_summary.write('\tTRUE')
fout_detailed.write(
'{}\t{}\tEXPLICIT_UPDATE:DISBANDED\t\n'.format(
prev_rid, prev_gtdb_sp))
else:
fout_summary.write('\tFALSE')
# check if genome cluster has new genomes assembled from the type strain of the species
sp_gids = prev_genomes.sp_clusters[prev_rid]
if prev_rid in new_updated_sp_clusters:
sp_gids = sp_gids.union(new_updated_sp_clusters[prev_rid])
new_ts = new_type_strain_gids.intersection(sp_gids)
if new_ts:
new_type_strain.add(prev_rid)
fout_detailed.write(
'{}\t{}\tNEW_TYPE_STRAINS:NEW\tSpecies cluster has {:,} new genomes from type strain: {}\n'
.format(prev_rid, prev_gtdb_sp, len(new_ts),
','.join(new_ts)))
fout_summary.write(f'\t{len(new_ts)}')
# check if representative has changed
if (prev_rid in unchanged_genome and prev_rid in unchanged_sp
and prev_rid in unchanged_type_strain
and prev_rid in unchanged_domain
and prev_rid not in disbanded_rids):
fout_summary.write('\tNO')
else:
fout_summary.write('\tYES')
num_rep_changes += 1
fout_summary.write('\n')
else:
lost_genome.add(prev_rid)
fout_summary.write('\t{}\t{}\t{}\t{}\t{}\t{}\n'.format(
'LOST', 'N/A', 'N/A', 'N/A', 'N/A', 'YES'))
fout_detailed.write(
f'{prev_rid}\t{prev_gtdb_sp}\tGENOMIC_CHANGE:LOST\tGenome not present in current GTDB release\n'
)
num_rep_changes += 1
fout_summary.close()
fout_detailed.close()
num_prev_sp_clusters = len(prev_genomes.sp_clusters)
num_rep_changes_perc = num_rep_changes * 100.0 / num_prev_sp_clusters
self.logger.info(
f' - identified {num_rep_changes:,} ({num_rep_changes_perc:.1f}%) species with a change to the representative genome.'
)
self.logger.info('Genomic changes:')
unchanged_perc = len(unchanged_genome) * 100.0 / num_prev_sp_clusters
updated_perc = len(updated_genome) * 100.0 / num_prev_sp_clusters
lost_perc = len(lost_genome) * 100.0 / num_prev_sp_clusters
self.logger.info(
f' unchanged_genome: {len(unchanged_genome):,} ({unchanged_perc:.1f}%)'
)
self.logger.info(
f' updated_genome: {len(updated_genome):,} ({updated_perc:.1f}%)')
self.logger.info(
f' lost_genome: {len(lost_genome):,} ({lost_perc:.1f}%)')
self.logger.info('NCBI species assignment changes:')
cur_sp_count = len(unchanged_genome) + len(updated_genome)
unchanged_sp_perc = len(unchanged_sp) * 100.0 / cur_sp_count
reassigned_sp_perc = len(reassigned_sp) * 100.0 / cur_sp_count
self.logger.info(
f' unchanged_sp: {len(unchanged_sp):,} ({unchanged_sp_perc:.1f}%)'
)
self.logger.info(
f' reassigned_sp: {len(reassigned_sp):,} ({reassigned_sp_perc:.1f}%)'
)
self.logger.info('Status of type strain genome declarations:')
prev_ts_count = len(unchanged_type_strain) + len(lost_type_strain)
unchanged_type_strain_perc = len(
unchanged_type_strain) * 100.0 / prev_ts_count
lost_type_strain_perc = len(lost_type_strain) * 100.0 / prev_ts_count
gain_type_strain_perc = len(gain_type_strain) * 100.0 / prev_ts_count
new_type_strain_perc = len(new_type_strain) * 100.0 / prev_ts_count
self.logger.info(
f' unchanged_type_strain: {len(unchanged_type_strain):,} ({unchanged_type_strain_perc:.1f}%)'
)
self.logger.info(
f' lost_type_strain: {len(lost_type_strain):,} ({lost_type_strain_perc:.1f}%)'
)
self.logger.info(
f' gain_type_strain: {len(gain_type_strain):,} ({gain_type_strain_perc:.1f}%)'
)
self.logger.info(
f' new_type_strain: {len(new_type_strain):,} ({new_type_strain_perc:.1f}%)'
)
self.logger.info('GTDB domain assignment change:')
unchanged_domain_perc = len(
unchanged_domain) * 100.0 / num_prev_sp_clusters
changed_domain_perc = len(
changed_domain) * 100.0 / num_prev_sp_clusters
self.logger.info(
f' unchanged: {len(unchanged_domain):,} ({unchanged_domain_perc:.1f}%)'
)
self.logger.info(
f' reassigned: {len(changed_domain):,} ({changed_domain_perc:.1f}%)'
)
self.logger.info(
'Identified {:,} representatives marked as anomalous assemblies at NCBI.'
.format(len(ncbi_anomalous_assembly)))
self.logger.info(
'Identified {:,} GTDB clusters to be disbanded.'.format(
disbanded_count))
