def identify(self,
genomes,
out_dir,
prefix,
force):
"""Identify marker genes in genomes."""
check_dependencies(['prodigal', 'hmmsearch'])
try:
self.logger.info('Identifying markers in %d genomes with %d threads.' % (len(genomes),
self.cpus))
self.logger.info("Running Prodigal to identify genes.")
self.marker_gene_dir = os.path.join(out_dir, DIR_MARKER_GENE)
prodigal = Prodigal(self.cpus,
False,
self.marker_gene_dir,
self.protein_file_suffix,
self.nt_gene_file_suffix,
self.gff_file_suffix,
force)
genome_dictionary = prodigal.run(genomes)
# 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._report_identified_marker_genes(
genome_dictionary, out_dir, self.marker_gene_dir, prefix)
except IOError as e:
self.logger.error(str(e))
self.logger.error("GTDB-Tk has encountered an error.")
except Exception as e:
self.logger.error(str(e))
raise
def infer(self, options):
"""Infer tree from MSA."""
check_file_exists(options.msa_file)
make_sure_path_exists(options.out_dir)
if options.cpus > 1:
check_dependencies(['FastTreeMP'])
else:
check_dependencies(['FastTree'])
self.logger.info('Inferring tree with FastTree using %s+GAMMA.' %
options.prot_model)
if hasattr(options, 'suffix'):
output_tree = os.path.join(
options.out_dir,
options.prefix + options.suffix + '.unrooted.tree')
tree_log = os.path.join(
options.out_dir, options.prefix + options.suffix + '.tree.log')
fasttree_log = os.path.join(
options.out_dir,
options.prefix + options.suffix + '.fasttree.log')
else:
output_tree = os.path.join(options.out_dir,
options.prefix + '.unrooted.tree')
tree_log = os.path.join(options.out_dir,
options.prefix + '.tree.log')
fasttree_log = os.path.join(options.out_dir,
options.prefix + '.fasttree.log')
if options.prot_model == 'JTT':
model_str = ''
elif options.prot_model == 'WAG':
model_str = ' -wag'
elif options.prot_model == 'LG':
model_str = ' -lg'
support_str = ''
if options.no_support:
support_str = ' -nosupport'
gamma_str = ' -gamma'
if options.no_gamma:
gamma_str = ''
cmd = '-quiet%s%s%s -log %s %s > %s 2> %s' % (
support_str, model_str, gamma_str, tree_log, options.msa_file,
output_tree, fasttree_log)
if options.cpus > 1:
cmd = 'FastTreeMP ' + cmd
else:
cmd = 'FastTree ' + cmd
self.logger.info('Running: %s' % cmd)
os.system(cmd)
self.logger.info('Done.')
def parse_options(self, options):
"""Parse user options and call the correct pipeline(s)"""
if (options.subparser_name == 'de_novo_wf'):
check_dependencies(['prodigal', 'hmmalign'])
if (options.cpus > 1):
check_dependencies(['FastTreeMP'])
else:
check_dependencies(['FastTree'])
self.identify(options)
options.identify_dir = options.out_dir
self.align(options)
if options.bac120_ms:
options.suffix = ".bac120"
else:
options.suffix = ".ar122"
if options.skip_gtdb_refs:
options.msa_file = os.path.join(
options.out_dir, Config.INTERMEDIATE_RESULTS,
options.prefix + options.suffix + ".user_msa.fasta")
else:
options.msa_file = os.path.join(
options.out_dir, Config.INTERMEDIATE_RESULTS,
options.prefix + options.suffix + ".msa.fasta")
self.infer(options)
options.input_tree = os.path.join(
options.out_dir, Config.INTERMEDIATE_RESULTS,
options.prefix + options.suffix + ".unrooted.tree")
options.output_tree = os.path.join(
options.out_dir,
options.prefix + options.suffix + ".rooted.tree")
self.root(options)
self.decorate(options)
elif (options.subparser_name == 'classify_wf'):
check_dependencies(
['prodigal', 'hmmalign', 'pplacer', 'guppy', 'fastANI'])
self.identify(options)
options.identify_dir = options.out_dir
options.align_dir = options.out_dir
options.taxa_filter = None
options.custom_msa_filters = False
options.min_consensus = None
options.min_perc_taxa = None
options.skip_gtdb_refs = False
options.cols_per_gene = None
options.max_consensus = None
options.rnd_seed = None
self.align(options)
self.classify(options)
elif (options.subparser_name == 'identify'):
self.identify(options)
elif (options.subparser_name == 'align'):
self.align(options)
elif (options.subparser_name == 'infer'):
self.infer(options)
elif (options.subparser_name == 'classify'):
self.classify(options)
elif (options.subparser_name == 'root'):
self.root(options)
elif (options.subparser_name == 'decorate'):
self.decorate(options)
elif (options.subparser_name == 'trim_msa'):
self.trim_msa(options)
elif (options.subparser_name == 'test'):
self.run_test(options)
elif (options.subparser_name == 'check_install'):
self.check_install()
else:
self.logger.error('Unknown GTDB-Tk command: "' +
options.subparser_name + '"\n')
sys.exit()
return 0
def parse_options(self, options):
"""Parse user options and call the correct pipeline(s)"""
if (options.subparser_name == 'de_novo_wf'):
check_dependencies(['prodigal', 'hmmalign'])
if (options.cpus > 1):
check_dependencies(['FastTreeMP'])
else:
check_dependencies(['FastTree'])
self.identify(options)
options.identify_dir = options.out_dir
self.align(options)
if options.bac120_ms:
options.suffix = "bac120"
else:
options.suffix = "ar122"
if options.skip_gtdb_refs:
if options.suffix == 'bac120':
options.msa_file = os.path.join(
options.out_dir,
PATH_BAC120_USER_MSA.format(prefix=options.prefix))
elif options.suffix == 'ar122':
options.msa_file = os.path.join(
options.out_dir,
PATH_AR122_USER_MSA.format(prefix=options.prefix))
else:
self.logger.error(
'There was an error determining the marker set.')
raise GenomeMarkerSetUnknown
else:
if options.suffix == 'bac120':
options.msa_file = os.path.join(
options.out_dir,
PATH_BAC120_MSA.format(prefix=options.prefix))
elif options.suffix == 'ar122':
options.msa_file = os.path.join(
options.out_dir,
PATH_AR122_MSA.format(prefix=options.prefix))
else:
self.logger.error(
'There was an error determining the marker set.')
raise GenomeMarkerSetUnknown
self.infer(options)
if options.suffix == 'bac120':
options.input_tree = os.path.join(
options.out_dir,
PATH_BAC120_UNROOTED_TREE.format(prefix=options.prefix))
options.output_tree = os.path.join(
options.out_dir,
PATH_BAC120_ROOTED_TREE.format(prefix=options.prefix))
elif options.suffix == 'ar122':
options.input_tree = os.path.join(
options.out_dir,
PATH_AR122_UNROOTED_TREE.format(prefix=options.prefix))
options.output_tree = os.path.join(
options.out_dir,
PATH_AR122_ROOTED_TREE.format(prefix=options.prefix))
else:
self.logger.error(
'There was an error determining the marker set.')
raise GenomeMarkerSetUnknown
self.root(options)
self.decorate(options)
elif (options.subparser_name == 'classify_wf'):
check_dependencies(
['prodigal', 'hmmalign', 'pplacer', 'guppy', 'fastANI'])
self.identify(options)
options.identify_dir = options.out_dir
options.align_dir = options.out_dir
options.taxa_filter = None
options.custom_msa_filters = False
options.skip_trimming = False # Added here due to the other mutex argument being include above.
options.min_consensus = None
options.min_perc_taxa = None
options.skip_gtdb_refs = False
options.cols_per_gene = None
options.max_consensus = None
options.rnd_seed = None
self.align(options)
self.classify(options)
elif (options.subparser_name == 'identify'):
self.identify(options)
elif (options.subparser_name == 'align'):
self.align(options)
elif (options.subparser_name == 'infer'):
self.infer(options)
elif (options.subparser_name == 'classify'):
self.classify(options)
elif (options.subparser_name == 'root'):
self.root(options)
elif (options.subparser_name == 'decorate'):
self.decorate(options)
elif (options.subparser_name == 'trim_msa'):
self.trim_msa(options)
elif (options.subparser_name == 'export_msa'):
self.export_msa(options)
elif (options.subparser_name == 'test'):
self.run_test(options)
elif (options.subparser_name == 'check_install'):
self.check_install()
else:
self.logger.error('Unknown GTDB-Tk command: "' +
options.subparser_name + '"\n')
sys.exit()
return 0
def infer(self, options):
"""Infer tree from MSA."""
check_file_exists(options.msa_file)
make_sure_path_exists(options.out_dir)
if options.cpus > 1:
check_dependencies(['FastTreeMP'])
os.environ['OMP_NUM_THREADS'] = '%d' % options.cpus
else:
check_dependencies(['FastTree'])
self.logger.info('Inferring tree with FastTree using %s+GAMMA.' %
options.prot_model)
if hasattr(options, 'suffix'):
output_tree = os.path.join(
options.out_dir,
PATH_MARKER_UNROOTED_TREE.format(prefix=options.prefix,
marker=options.suffix))
tree_log = os.path.join(
options.out_dir,
PATH_MARKER_TREE_LOG.format(prefix=options.prefix,
marker=options.suffix))
fasttree_log = os.path.join(
options.out_dir,
PATH_MARKER_FASTTREE_LOG.format(prefix=options.prefix,
marker=options.suffix))
else:
output_tree = os.path.join(
options.out_dir,
PATH_UNROOTED_TREE.format(prefix=options.prefix))
tree_log = os.path.join(
options.out_dir, PATH_TREE_LOG.format(prefix=options.prefix))
fasttree_log = os.path.join(
options.out_dir,
PATH_FASTTREE_LOG.format(prefix=options.prefix))
make_sure_path_exists(os.path.dirname(output_tree))
make_sure_path_exists(os.path.dirname(tree_log))
make_sure_path_exists(os.path.dirname(fasttree_log))
if options.prot_model == 'JTT':
model_str = ''
elif options.prot_model == 'WAG':
model_str = ' -wag'
elif options.prot_model == 'LG':
model_str = ' -lg'
support_str = ''
if options.no_support:
support_str = ' -nosupport'
gamma_str = ' -gamma'
gamma_str_info = '+GAMMA'
if options.no_gamma:
gamma_str = ''
gamma_str_info = ''
self.logger.info('Inferring tree with FastTree using {}.'.format(
options.prot_model, gamma_str_info))
cmd = '-quiet%s%s%s -log %s %s > %s 2> %s' % (
support_str, model_str, gamma_str, tree_log, options.msa_file,
output_tree, fasttree_log)
if options.cpus > 1:
cmd = 'FastTreeMP ' + cmd
else:
cmd = 'FastTree ' + cmd
self.logger.info('Running: %s' % cmd)
os.system(cmd)
self.logger.info('Done.')
