def call_genes(self, options):
"""Call genes command"""
self.logger.info('')
self.logger.info('*******************************************************************************')
self.logger.info(' [CompareM - call_genes] Identifying genes within genomes.')
self.logger.info('*******************************************************************************')
make_sure_path_exists(options.output_dir)
genome_files = self._genome_files(options.genome_dir, options.genome_ext)
if not genome_files:
self.logger.warning(' [Warning] No genome files found. Check the --genome_ext flag used to identify genomes.')
sys.exit()
prodigal = Prodigal(options.cpus)
summary_stats = prodigal.run(genome_files, False, options.force_table, False, options.output_dir)
# write gene calling summary
fout = open(os.path.join(options.output_dir, 'call_genes.summary.tsv'), 'w')
fout.write('Genome Id\tSelected translation table\tTable 4 coding density\tTable 11 coding density\n')
for genome_id, stats in summary_stats.iteritems():
fout.write('%s\t%d\t%.2f%%\t%.2f%%\n' % (genome_id,
stats.best_translation_table,
stats.coding_density_4,
stats.coding_density_11))
fout.close()
self.logger.info('')
self.logger.info(' Identified genes written to: %s' % options.output_dir)
self.time_keeper.print_time_stamp()
def call_genes(self, options):
"""Call genes command"""
make_sure_path_exists(options.output_dir)
genome_files = self._input_files(options.input_genomes, options.file_ext)
prodigal = Prodigal(options.cpus, not options.silent)
summary_stats = prodigal.run(genome_files,
options.output_dir,
called_genes=False,
translation_table=options.force_table,
meta=False,
closed_ends=True)
# write gene calling summary
fout = open(os.path.join(options.output_dir, 'call_genes.summary.tsv'), 'w')
fout.write('Genome Id\tSelected translation table\tTable 4 coding density\tTable 11 coding density\n')
for genome_id, stats in summary_stats.items():
fout.write('%s\t%d\t%.2f%%\t%.2f%%\n' % (genome_id,
stats.best_translation_table,
stats.coding_density_4,
stats.coding_density_11))
fout.close()
self.logger.info('Identified genes written to: %s' % options.output_dir)
def call_genes(self, options):
"""Call genes command"""
self.logger.info('')
self.logger.info('*******************************************************************************')
self.logger.info(' [RefineM - call_genes] Identifying genes within genomes.')
self.logger.info('*******************************************************************************')
check_dir_exists(options.genome_nt_dir)
make_sure_path_exists(options.output_dir)
genome_files = self._genome_files(options.genome_nt_dir, options.genome_ext)
if not self._check_nuclotide_seqs(genome_files):
self.logger.warning('[Warning] All files must contain nucleotide sequences.')
sys.exit()
# call genes in genomes
prodigal = Prodigal(options.cpus)
prodigal.run(genome_files, options.output_dir)
self.logger.info(' Genes in genomes written to: %s' % options.output_dir)
# call genes in unbinned scaffolds
if options.unbinned_file:
unbinned_output_dir = os.path.join(options.output_dir, 'unbinned')
prodigal.run([options.unbinned_file], unbinned_output_dir, meta=True)
self.logger.info(' Genes in unbinned scaffolds written to: %s' % unbinned_output_dir)
self.time_keeper.print_time_stamp()
def run(self, input_dir, tmp_dir, threads):
# get path to all unprocessed genome files
print 'Reading genomes.'
genome_files = []
for genome_dir in os.listdir(input_dir):
cur_genome_dir = os.path.join(input_dir, genome_dir)
if not os.path.isdir(cur_genome_dir):
continue
for assembly_id in os.listdir(cur_genome_dir):
assembly_dir = os.path.join(cur_genome_dir, assembly_id)
genome_id = assembly_id[0:assembly_id.find('_', 4)]
# check if prodigal has already been called
if False:
# for safety, I am just recalling genes for all genomes right now,
# but this is very efficient
aa_gene_file = os.path.join(assembly_dir, 'prodigal', genome_id + '_protein.faa')
if os.path.exists(aa_gene_file):
# verify checksum
checksum_file = aa_gene_file + '.sha256'
if os.path.exists(checksum_file):
checksum = sha256(aa_gene_file)
cur_checksum = open(checksum_file).readline().strip()
if checksum == cur_checksum:
continue
genome_file = os.path.join(assembly_dir, assembly_id + '_genomic.fna')
if os.path.exists(genome_file):
if os.stat(genome_file).st_size == 0:
print '[Warning] Genome file appears to be empty: %s' % genome_file
else:
genome_files.append(genome_file)
print ' Number of unprocessed genomes: %d' % len(genome_files)
# run prodigal on each genome
print 'Running prodigal.'
prodigal = Prodigal(cpus=threads)
summary_stats = prodigal.run(genome_files, output_dir=tmp_dir)
# move results into individual genome directories
print 'Moving files and calculating checksums.'
for genome_file in genome_files:
genome_path, genome_id = ntpath.split(genome_file)
genome_id = remove_extension(genome_id)
aa_gene_file = os.path.join(tmp_dir, genome_id + '_genes.faa')
nt_gene_file = os.path.join(tmp_dir, genome_id + '_genes.fna')
gff_file = os.path.join(tmp_dir, genome_id + '.gff')
genome_root = genome_id[0:genome_id.find('_', 4)]
prodigal_path = os.path.join(genome_path, 'prodigal')
if not os.path.exists(prodigal_path):
os.makedirs(prodigal_path)
new_aa_gene_file = os.path.join(prodigal_path, genome_root + '_protein.faa')
new_nt_gene_file = os.path.join(prodigal_path, genome_root + '_protein.fna')
new_gff_file = os.path.join(prodigal_path, genome_root + '_protein.gff')
os.system('mv %s %s' % (aa_gene_file, new_aa_gene_file))
os.system('mv %s %s' % (nt_gene_file, new_nt_gene_file))
os.system('mv %s %s' % (gff_file, new_gff_file))
# save translation table information
translation_table_file = os.path.join(prodigal_path, 'prodigal_translation_table.tsv')
fout = open(translation_table_file, 'w')
fout.write('%s\t%d\n' % ('best_translation_table', summary_stats[genome_id].best_translation_table))
fout.write('%s\t%.2f\n' % ('coding_density_4', summary_stats[genome_id].coding_density_4 * 100))
fout.write('%s\t%.2f\n' % ('coding_density_11', summary_stats[genome_id].coding_density_11 * 100))
fout.close()
checksum = sha256(new_aa_gene_file)
fout = open(new_aa_gene_file + '.sha256', 'w')
fout.write(checksum)
fout.close()
