def __init__(self, args, run=run, progress=progress):
self.run = run
self.progress = progress
A = lambda x, t: t(args.__dict__[x]) if x in args.__dict__ else None
null = lambda x: x
self.contigs_db_path = A('contigs_db', null)
self.num_threads = A('num_threads', null)
self.hmm_program = A('hmmer_program', null) or 'hmmsearch'
self.pfam_data_dir = A('pfam_data_dir', null)
# load_catalog will populate this
self.function_catalog = {}
filesnpaths.is_program_exists(self.hmm_program)
utils.is_contigs_db(self.contigs_db_path)
if not self.pfam_data_dir:
self.pfam_data_dir = os.path.join(os.path.dirname(anvio.__file__),
'data/misc/Pfam')
# here, in the process of checking whether Pfam has been downloaded into the pfam_data_dir,
# we also decompress and hmmpress the profile if it is currently gzipped
self.is_database_exists()
self.run.info('Pfam database directory', self.pfam_data_dir)
self.get_version()
self.load_catalog()
def __init__(self, args, run=run, progress=progress):
self.args = args
self.run = run
self.progress = progress
self.pfam_data_dir = args.pfam_data_dir
filesnpaths.is_program_exists('hmmpress')
if self.pfam_data_dir and args.reset:
raise ConfigError(
"You are attempting to run Pfam setup on a non-default data directory (%s) using the --reset flag. "
"To avoid automatically deleting a directory that may be important to you, anvi'o refuses to reset "
"directories that have been specified with --pfam-data-dir. If you really want to get rid of this "
"directory and regenerate it with Pfam data inside, then please remove the directory yourself using "
"a command like `rm -r %s`. We are sorry to make you go through this extra trouble, but it really is "
"the safest way to handle things." %
(self.pfam_data_dir, self.pfam_data_dir))
if not self.pfam_data_dir:
self.pfam_data_dir = os.path.join(os.path.dirname(anvio.__file__),
'data/misc/Pfam')
filesnpaths.is_output_dir_writable(os.path.dirname(self.pfam_data_dir))
if not args.reset and not anvio.DEBUG:
self.is_database_exists()
filesnpaths.gen_output_directory(self.pfam_data_dir,
delete_if_exists=args.reset)
self.database_url = "http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release"
self.files = [
'Pfam-A.hmm.gz', 'Pfam.version.gz', 'Pfam-A.clans.tsv.gz'
]
def __init__(self,
db_path,
num_threads_to_use=1,
run=run,
progress=progress,
initializing_for_deletion=False,
just_do_it=False,
hmm_program_to_use='hmmscan',
hmmer_output_directory=None,
get_domain_table_output=False):
self.num_threads_to_use = num_threads_to_use
self.db_path = db_path
self.just_do_it = just_do_it
self.hmm_program = hmm_program_to_use or 'hmmscan'
self.hmmer_output_dir = hmmer_output_directory
self.hmmer_desired_output = (
'table', 'domtable') if get_domain_table_output else 'table'
utils.is_contigs_db(self.db_path)
filesnpaths.is_program_exists(self.hmm_program)
self.contigs_db_hash = db.DB(
self.db_path, utils.get_required_version_for_db(
self.db_path)).get_meta_value('contigs_db_hash')
Table.__init__(self, self.db_path, anvio.__contigs__version__, run,
progress)
self.init_gene_calls_dict()
if not len(self.gene_calls_dict):
if self.genes_are_called:
self.run.warning(
"Tables in this contigs database that should contain gene calls are empty despite the fact that "
"you didn't skip the gene calling step while generating this contigs database. This probably means "
"that the gene caller did not find any genes among contigs. This is OK for now. But might explode "
"later. If it does explode and you decide to let us know about that problem, please remember to mention "
"this warning. By the way, this warning probably has been seen by like only 2 people on the planet. Who "
"works with contigs with no gene calls? A better implementation of anvi'o will unite researchers who "
"study weird stuff.")
else:
self.run.warning(
"It seems you have skipped gene calling step while generating your contigs database, and you have no "
"genes calls in tables that should contain gene calls. Anvi'o will let you go with this since some HMM "
"sources only operate on DNA sequences, and at this point it doesn't know which HMMs you wish to run. "
"If the lack of genes causes a problem, you will get another error message later probably :/"
)
if not initializing_for_deletion:
self.set_next_available_id(t.hmm_hits_table_name)
def __init__(self, args, run=run, progress=progress):
self.args = args
self.run = run
self.progress = progress
self.pfam_data_dir = args.pfam_data_dir
filesnpaths.is_program_exists('hmmpress')
if not self.pfam_data_dir:
self.pfam_data_dir = os.path.join(os.path.dirname(anvio.__file__), 'data/misc/Pfam')
if not args.reset:
self.is_database_exists()
filesnpaths.gen_output_directory(self.pfam_data_dir, delete_if_exists=args.reset)
self.database_url = "http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release"
self.files = ['Pfam-A.hmm.gz', 'Pfam.version.gz', 'Pfam-A.clans.tsv.gz']
def __init__(self, args, run=run, progress=progress):
self.args = args
self.run = run
self.progress = progress
self.pfam_data_dir = args.pfam_data_dir
filesnpaths.is_program_exists('hmmpress')
if not self.pfam_data_dir:
self.pfam_data_dir = os.path.join(os.path.dirname(anvio.__file__),
'data/misc/Pfam')
if not args.reset:
self.is_database_exists()
filesnpaths.gen_output_directory(self.pfam_data_dir,
delete_if_exists=args.reset)
self.database_url = "http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release"
self.files = [
'Pfam-A.hmm.gz', 'Pfam.version.gz', 'Pfam-A.clans.tsv.gz'
]
def __init__(self, args, run=run, progress=progress):
self.args = args
self.run = run
self.progress = progress
self.contigs_db_path = args.contigs_db
self.num_threads = args.num_threads
self.pfam_data_dir = args.pfam_data_dir
# load_catalog will populate this
self.function_catalog = {}
filesnpaths.is_program_exists('hmmscan')
utils.is_contigs_db(self.contigs_db_path)
if not self.pfam_data_dir:
self.pfam_data_dir = os.path.join(os.path.dirname(anvio.__file__), 'data/misc/Pfam')
self.is_database_exists()
self.run.info('Pfam database directory', self.pfam_data_dir)
self.get_version()
self.load_catalog()
def __init__(self, args, run=run, progress=progress):
self.args = args
self.run = run
self.progress = progress
self.contigs_db_path = args.contigs_db
self.num_threads = args.num_threads
self.pfam_data_dir = args.pfam_data_dir
# load_catalog will populate this
self.function_catalog = {}
filesnpaths.is_program_exists('hmmscan')
utils.is_contigs_db(self.contigs_db_path)
if not self.pfam_data_dir:
self.pfam_data_dir = os.path.join(os.path.dirname(anvio.__file__),
'data/misc/Pfam')
self.is_database_exists()
self.run.info('Pfam database directory', self.pfam_data_dir)
self.get_version()
self.load_catalog()
def check_sge_binaries(self):
filesnpaths.is_program_exists('qsub')
filesnpaths.is_program_exists('qstat')
def check_sge_binaries(self):
filesnpaths.is_program_exists('qsub')
filesnpaths.is_program_exists('qstat')