def identify(self, genomes, tln_tables, out_dir, prefix, force):
"""Identify marker genes in genomes.
Parameters
----------
genomes : dict
Genome IDs as the key, path to genome file as value.
tln_tables: Dict[str, int]
Genome ID -> translation table mapping for those user-specified.
out_dir : str
Path to the output directory.
prefix : str
Prefix to append to generated files.
force : bool
Overwrite any existing files.
Raises
------
GTDBTkException
If an exception is encountered during the identify step.
"""
check_dependencies(['prodigal', 'hmmsearch'])
self.logger.info('Identifying markers in %d genomes with %d threads.' %
(len(genomes), self.cpus))
self.marker_gene_dir = os.path.join(out_dir, DIR_MARKER_GENE)
prodigal = Prodigal(self.cpus, self.marker_gene_dir,
self.protein_file_suffix, self.nt_gene_file_suffix,
self.gff_file_suffix, force)
self.logger.info("Running Prodigal {} to identify genes.".format(
prodigal.version))
genome_dictionary = prodigal.run(genomes, tln_tables)
# annotated genes against TIGRFAM and Pfam databases
self.logger.info("Identifying TIGRFAM protein families.")
gene_files = [
genome_dictionary[db_genome_id]['aa_gene_path']
for db_genome_id in genome_dictionary.keys()
]
tigr_search = TigrfamSearch(self.cpus, self.tigrfam_hmms,
self.protein_file_suffix,
self.tigrfam_suffix,
self.tigrfam_top_hit_suffix,
self.checksum_suffix, self.marker_gene_dir)
tigr_search.run(gene_files)
self.logger.info("Identifying Pfam protein families.")
pfam_search = PfamSearch(self.cpus, self.pfam_hmm_dir,
self.protein_file_suffix, self.pfam_suffix,
self.pfam_top_hit_suffix,
self.checksum_suffix, self.marker_gene_dir)
pfam_search.run(gene_files)
self.logger.info("Annotations done using HMMER {}.".format(
tigr_search.version))
self._report_identified_marker_genes(genome_dictionary, out_dir,
prefix)
def identify(self, genomes, tln_tables, out_dir, prefix, force, genes,
write_single_copy_genes):
"""Identify marker genes in genomes.
Parameters
----------
genomes : dict
Genome IDs as the key, path to genome file as value.
tln_tables: Dict[str, int]
Genome ID -> translation table mapping for those user-specified.
out_dir : str
Path to the output directory.
prefix : str
Prefix to append to generated files.
force : bool
Overwrite any existing files.
genes : bool
True if the supplied genomes are called genes, False otherwise.
write_single_copy_genes : bool
Write unique AR53/BAC120 marker files to disk.
Raises
------
GTDBTkException
If an exception is encountered during the identify step.
"""
check_dependencies(['prodigal', 'hmmsearch'])
self.logger.info(
f'Identifying markers in {len(genomes):,} genomes with '
f'{self.cpus} threads.')
self.marker_gene_dir = os.path.join(out_dir, DIR_MARKER_GENE)
self.failed_genomes = os.path.join(out_dir,
PATH_FAILS.format(prefix=prefix))
if not genes:
prodigal = Prodigal(self.cpus, self.failed_genomes,
self.marker_gene_dir, self.protein_file_suffix,
self.nt_gene_file_suffix, self.gff_file_suffix,
force)
self.logger.log(
Config.LOG_TASK,
f'Running Prodigal {prodigal.version} to identify genes.')
genome_dictionary = prodigal.run(genomes, tln_tables)
else:
self.logger.info(
'Using supplied genomes as called genes, skipping Prodigal.')
genome_dictionary = dict()
for gid, gpath in genomes.items():
genome_dictionary[gid] = {
'aa_gene_path': gpath,
'translation_table_path': None,
'nt_gene_path': None,
'best_translation_table': 'user_supplied',
'gff_path': None
}
# annotated genes against TIGRFAM and Pfam databases
self.logger.log(Config.LOG_TASK,
'Identifying TIGRFAM protein families.')
gene_files = [
genome_dictionary[db_genome_id]['aa_gene_path']
for db_genome_id in genome_dictionary.keys()
]
tigr_search = TigrfamSearch(self.cpus, self.tigrfam_hmms,
self.protein_file_suffix,
self.tigrfam_suffix,
self.tigrfam_top_hit_suffix,
self.checksum_suffix, self.marker_gene_dir)
tigr_search.run(gene_files)
self.logger.log(Config.LOG_TASK, 'Identifying Pfam protein families.')
pfam_search = PfamSearch(self.cpus, self.pfam_hmm_dir,
self.protein_file_suffix, self.pfam_suffix,
self.pfam_top_hit_suffix,
self.checksum_suffix, self.marker_gene_dir)
pfam_search.run(gene_files)
self.logger.info(
f'Annotations done using HMMER {tigr_search.version}.')
self.logger.log(Config.LOG_TASK,
'Summarising identified marker genes.')
self._report_identified_marker_genes(genome_dictionary, out_dir,
prefix, write_single_copy_genes)
def identify(self, genomes, out_dir, prefix, force, genes):
"""Identify marker genes in genomes.
Parameters
----------
genomes : dict
Genome IDs as the key, path to genome file as value.
out_dir : str
Path to the output directory.
prefix : str
Prefix to append to generated files.
force : bool
Overwrite any existing files.
genes : bool
True if the supplied genomes are called genes, False otherwise.
Raises
------
GTDBTkException
If an exception is encountered during the identify step.
"""
check_dependencies(['prodigal', 'hmmsearch'])
self.logger.info('Identifying markers in %d genomes with %d threads.' %
(len(genomes), self.cpus))
marker_gene_dir = os.path.join(out_dir, DIR_MARKER_GENE)
if not genes:
self.logger.info("Running Prodigal to identify genes.")
prodigal = Prodigal(self.cpus, False, marker_gene_dir,
self.protein_file_suffix,
self.nt_gene_file_suffix, self.gff_file_suffix,
force)
genome_dictionary = prodigal.run(genomes)
else:
self.logger.info(
'Using supplied genomes as called genes, skipping Prodigal.')
genome_dictionary = dict()
for gid, gpath in genomes.items():
genome_dictionary[gid] = {
'aa_gene_path': gpath,
'translation_table_path': None,
'nt_gene_path': None,
'best_translation_table': 'user_supplied',
'gff_path': None
}
gene_files = [(db_genome_id,
genome_dictionary[db_genome_id]['aa_gene_path'])
for db_genome_id in genome_dictionary.keys()]
# annotated genes against TIGRFAM and Pfam databases
self.logger.info("Identifying TIGRFAM protein families.")
tigr_search = TigrfamSearch(self.cpus, self.tigrfam_hmms,
self.protein_file_suffix,
self.tigrfam_suffix,
self.tigrfam_top_hit_suffix,
self.checksum_suffix, marker_gene_dir)
tigr_search.run(gene_files)
self.logger.info("Identifying Pfam protein families.")
pfam_search = PfamSearch(self.cpus, self.pfam_hmm_dir,
self.protein_file_suffix, self.pfam_suffix,
self.pfam_top_hit_suffix,
self.checksum_suffix, marker_gene_dir)
pfam_search.run(gene_files)
self._report_identified_marker_genes(genome_dictionary, out_dir,
prefix)