def _path_to_identify_data(self, identity_dir, warn=True):
"""Get path to genome data produced by 'identify' command."""
marker_gene_dir = os.path.join(identity_dir, DIR_MARKER_GENE)
genomic_files = {}
lq_gids = list()
for gid in os.listdir(marker_gene_dir):
gid_dir = os.path.join(marker_gene_dir, gid)
if not os.path.isdir(gid_dir):
continue
aa_gene_path = os.path.join(gid_dir,
gid + self.protein_file_suffix)
# Check if any genes were called
if os.path.getsize(aa_gene_path) < 1:
lq_gids.append(gid)
else:
genomic_files[gid] = {
'aa_gene_path':
aa_gene_path,
'translation_table_path':
TlnTableFile.get_path(gid_dir, gid),
'nt_gene_path':
os.path.join(gid_dir, gid + self.nt_gene_file_suffix),
'gff_path':
os.path.join(gid_dir, gid + self.gff_file_suffix)
}
if len(lq_gids) > 0 and warn:
self.logger.warning(
f'Excluding {len(lq_gids)} genomes '
f'in the identify directory which have no genes '
f'called (see gtdbtk.warnings.log)')
self.warnings.warning(
f'Excluding the following {len(lq_gids)} genomes '
f'which were found in the identify directory '
f'with no genes called.')
for lq_gid in lq_gids:
self.warnings.info(lq_gid)
return genomic_files
def _run_prodigal(self, genome_id, fasta_path, usr_tln_table):
"""Run Prodigal.
Parameters
----------
fasta_path : str
Path to FASTA file to process.
usr_tln_table : int
User-specified translation table, None if automatic.
:return
False if an error occurred.
"""
# Set the paths for output files.
output_dir = os.path.join(self.marker_gene_dir, genome_id)
aa_gene_file = os.path.join(output_dir,
genome_id + self.protein_file_suffix)
nt_gene_file = os.path.join(output_dir,
genome_id + self.nt_gene_file_suffix)
gff_file = os.path.join(output_dir, genome_id + self.gff_file_suffix)
translation_table_file = os.path.join(
output_dir, 'prodigal_translation_table.tsv')
out_files = (nt_gene_file, gff_file, translation_table_file,
aa_gene_file)
# Check if this genome has already been processed (skip).
if all([file_has_checksum(x) for x in out_files]):
tln_table_file = TlnTableFile(translation_table_file)
tln_table_file.read()
self.warnings.info(f'Skipped Prodigal processing for: {genome_id}')
return aa_gene_file, nt_gene_file, gff_file, translation_table_file, tln_table_file.best_tln_table, True
# Run Prodigal
prodigal = BioLibProdigal(1, False)
summary_stats = prodigal.run([fasta_path],
output_dir,
called_genes=False,
translation_table=usr_tln_table)
# An error occurred in BioLib Prodigal.
if not summary_stats:
if self.force:
return None
else:
raise Exception(
"An error was encountered while running Prodigal.")
summary_stats = summary_stats[list(summary_stats.keys())[0]]
# rename output files to adhere to GTDB conventions and desired genome
# ID
shutil.move(summary_stats.aa_gene_file, aa_gene_file)
shutil.move(summary_stats.nt_gene_file, nt_gene_file)
shutil.move(summary_stats.gff_file, gff_file)
# save translation table information
tln_table_file = TlnTableFile(
translation_table_file,
best_tln_table=summary_stats.best_translation_table,
coding_density_4=round(summary_stats.coding_density_4 * 100, 2),
coding_density_11=round(summary_stats.coding_density_11 * 100, 2))
tln_table_file.write()
# Create a hash of each file
for out_file in out_files:
if out_file is not None:
with open(out_file + CHECKSUM_SUFFIX, 'w') as fh:
fh.write(sha256(out_file))
return aa_gene_file, nt_gene_file, gff_file, translation_table_file, summary_stats.best_translation_table, False