def _run_prodigal(self, genome_id, fasta_path):
"""Run Prodigal.
Parameters
----------
fasta_path : str
Path to FASTA file to process.
:return
False if an error occurred.
"""
output_dir = os.path.join(self.marker_gene_dir, genome_id)
prodigal = BioLibProdigal(1, False)
summary_stats = prodigal.run([fasta_path],
output_dir,
called_genes=self.proteins)
# 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
aa_gene_file = os.path.join(output_dir,
genome_id + self.protein_file_suffix)
shutil.move(summary_stats.aa_gene_file, aa_gene_file)
nt_gene_file = None
gff_file = None
translation_table_file = None
if not self.proteins:
nt_gene_file = os.path.join(output_dir,
genome_id + self.nt_gene_file_suffix)
shutil.move(summary_stats.nt_gene_file, nt_gene_file)
gff_file = os.path.join(output_dir,
genome_id + self.gff_file_suffix)
shutil.move(summary_stats.gff_file, gff_file)
# save translation table information
translation_table_file = os.path.join(
output_dir, 'prodigal_translation_table.tsv')
with open(translation_table_file, 'w') as fout:
fout.write('%s\t%d\n' % ('best_translation_table',
summary_stats.best_translation_table))
fout.write(
'%s\t%.2f\n' %
('coding_density_4', summary_stats.coding_density_4 * 100))
fout.write('%s\t%.2f\n' %
('coding_density_11',
summary_stats.coding_density_11 * 100))
# Create a hash of each file
for out_file in [
nt_gene_file, gff_file, translation_table_file, aa_gene_file
]:
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
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
def _run_prodigal(self, genome_id, fasta_path):
"""Run Prodigal.
Parameters
----------
fasta_path : str
Path to FASTA file to process.
:return
False if an error occurred.
"""
# Setup 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 = None
gff_file = None
translation_table_file = None
if not self.proteins:
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_SUFFIX)
# Return early if files are already done
if not self.proteins and file_has_checksum(aa_gene_file) and file_has_checksum(nt_gene_file) \
and file_has_checksum(gff_file) and file_has_checksum(translation_table_file):
best_tln_table = -1
with open(translation_table_file, 'r') as tln_f:
for line in tln_f.readlines():
cols = line.strip().split('\t')
if cols[0] == 'best_translation_table':
best_tln_table = int(cols[1])
break
if best_tln_table > 0:
self.logger.info(
'Skipping result from a previous run: {}'.format(
genome_id))
return aa_gene_file, nt_gene_file, gff_file, translation_table_file, best_tln_table
# Did not meet the conditions to skip processing this genome, call genes.
prodigal = BioLibProdigal(1, False)
summary_stats = prodigal.run([fasta_path],
output_dir,
called_genes=self.proteins)
# An error occured in BioLib Prodigal.
if not summary_stats:
if self.force:
return None
else:
raise GTDBTkExit(
"Prodigal failed to call genes for: {} "
"(to skip these genomes, re-run with --force)".format(
genome_id))
summary_stats = list(summary_stats.values())[0]
# rename output files to adhere to GTDB conventions and desired genome
# ID
shutil.move(summary_stats.aa_gene_file, aa_gene_file)
with open(aa_gene_file + CHECKSUM_SUFFIX, 'w') as f:
f.write(sha256(aa_gene_file))
if not self.proteins:
shutil.move(summary_stats.nt_gene_file, nt_gene_file)
with open(nt_gene_file + CHECKSUM_SUFFIX, 'w') as f:
f.write(sha256(nt_gene_file))
shutil.move(summary_stats.gff_file, gff_file)
with open(gff_file + CHECKSUM_SUFFIX, 'w') as f:
f.write(sha256(gff_file))
# save translation table information
translation_table_file = os.path.join(
output_dir, 'prodigal_translation_table.tsv')
with open(translation_table_file, 'w') as fout:
fout.write('%s\t%d\n' % ('best_translation_table',
summary_stats.best_translation_table))
fout.write(
'%s\t%.2f\n' %
('coding_density_4', summary_stats.coding_density_4 * 100))
fout.write('%s\t%.2f\n' %
('coding_density_11',
summary_stats.coding_density_11 * 100))
fout.write(
'%s\t%.2f\n' %
('probability_4', summary_stats.probability_4 * 100))
fout.write(
'%s\t%.2f\n' %
('probability_11', summary_stats.probability_11 * 100))
with open(translation_table_file + CHECKSUM_SUFFIX, 'w') as f:
f.write(sha256(translation_table_file))
return aa_gene_file, nt_gene_file, gff_file, translation_table_file, summary_stats.best_translation_table