def append(self,
collection_name,
collection_dict,
bins_info_dict={},
drop_collection=True):
utils.is_this_name_OK_for_database('collection name',
collection_name,
stringent=False)
for bin_name in collection_dict:
utils.is_this_name_OK_for_database('bin name',
bin_name,
stringent=False)
if bins_info_dict:
if set(collection_dict.keys()) - set(bins_info_dict.keys()):
raise ConfigError(
'Bins in the collection dict do not match to the ones in the bins info dict. '
'They do not have to be identical, but for each bin id, there must be a unique '
'entry in the bins informaiton dict. There is something wrong with your input :/'
)
if drop_collection:
# remove any pre-existing information for 'collection_name'
self.delete(collection_name)
num_splits_in_collection_dict = sum(
[len(splits) for splits in list(collection_dict.values())])
splits_in_collection_dict = set(
list(chain.from_iterable(list(collection_dict.values()))))
if len(splits_in_collection_dict) != num_splits_in_collection_dict:
raise ConfigError(
"TablesForCollections::append: %d of the split or contig IDs appear more than once in "
"your collections input. It is unclear to anvi'o how did you manage to do this, but we "
"cannot go anywhere with this :/" %
(num_splits_in_collection_dict -
len(splits_in_collection_dict)))
database = db.DB(self.db_path,
utils.get_required_version_for_db(self.db_path))
# how many clusters are defined in 'collection_dict'?
bin_names = list(collection_dict.keys())
if drop_collection:
db_entries = tuple([
collection_name, num_splits_in_collection_dict,
len(bin_names), ','.join(bin_names)
])
database._exec(
'''INSERT INTO %s VALUES (?,?,?,?)''' %
t.collections_info_table_name, db_entries)
if not bins_info_dict:
colors = utils.get_random_colors_dict(bin_names)
for bin_name in bin_names:
bins_info_dict[bin_name] = {
'html_color': colors[bin_name],
'source': 'UNKNOWN'
}
# populate bins info table.
db_entries = [(collection_name, b, bins_info_dict[b]['source'],
bins_info_dict[b]['html_color']) for b in bin_names]
database._exec_many(
'''INSERT INTO %s VALUES (?,?,?,?)''' %
t.collections_bins_info_table_name, db_entries)
# populate splits table
db_entries = []
for bin_name in collection_dict:
for split_name in collection_dict[bin_name]:
db_entries.append(
tuple([collection_name, split_name, bin_name]))
database._exec_many(
'''INSERT INTO %s VALUES (?,?,?)''' %
t.collections_splits_table_name, db_entries)
num_splits = len(db_entries)
# FIXME: This function can be called to populate the contigs database (via anvi-populate-collections), or
# the profile database. when it is contigs database, the superclass Table has the self.splits_info variable
# set when it is initialized. however, the Table instance is missing self.splis when it is initialized with
# the profile database. hence some special controls for contigs db (note that collections_contigs_table is
# only populated in the contigs database):
if self.db_type == 'contigs':
splits_only_in_collection_dict = [
c for c in splits_in_collection_dict
if c not in self.splits_info
]
splits_only_in_db = [
c for c in self.splits_info
if c not in splits_in_collection_dict
]
if len(splits_only_in_collection_dict):
self.run.warning('%d of %d splits found in "%s" results are not in the database. This may be OK,\
but you must be the judge of it. If this is somewhat surprising, please use caution\
and make sure all is fine before going forward with you analysis.'\
% (len(splits_only_in_collection_dict), len(splits_in_collection_dict), collection_name))
if len(splits_only_in_db):
self.run.warning('%d of %d splits found in the database were missing from the "%s" results. If this '
'does not make any sense, please make sure you know why before going any further.'\
% (len(splits_only_in_db), len(self.splits_info), collection_name))
# then populate contigs table.
db_entries = self.process_contigs(collection_name, collection_dict)
database._exec_many(
'''INSERT INTO %s VALUES (?,?,?,?)''' %
t.collections_contigs_table_name, db_entries)
database.disconnect()
num_bins = len(bin_names)
num_bins_to_report = 50
if not drop_collection:
bins_to_report = bin_names
bin_report_msg = "Here is a full list of the bin names added to this collection: {}.".format(
", ".join(bins_to_report))
elif num_bins <= num_bins_to_report:
bins_to_report = bin_names
bin_report_msg = "Here is a full list of the bin names in this collection: {}.".format(
", ".join(bins_to_report))
else:
bins_to_report = bin_names[:num_bins_to_report]
bin_report_msg = "Here is a list of the first {} bin names in this collection: {}.".format(
num_bins_to_report, ", ".join(bins_to_report))
if drop_collection:
self.run.info(
'Collections',
'The collection "%s" that describes %s splits and %s bins has been successfully added to the\
database at "%s". %s' %
(collection_name, pp(num_splits), pp(num_bins), self.db_path,
bin_report_msg),
mc='green')
else:
self.run.info(
'Collections',
'The existing collection "%s" updated, %s splits and %s bins has been successfully added to the\
database at "%s". %s' %
(collection_name, pp(num_splits), pp(num_bins), self.db_path,
bin_report_msg),
mc='green')
def append(self, collection_name, collection_dict, bins_info_dict={}):
utils.is_this_name_OK_for_database('collection name', collection_name, stringent=False)
for bin_name in collection_dict:
utils.is_this_name_OK_for_database('bin name', bin_name, stringent=False)
if bins_info_dict:
if set(collection_dict.keys()) - set(bins_info_dict.keys()):
raise ConfigError('Bins in the collection dict do not match to the ones in the bins info dict.\
They do not have to be identical, but for each bin id, there must be a unique\
entry in the bins informaiton dict. There is something wrong with your input :/')
# remove any pre-existing information for 'collection_name'
self.delete(collection_name)
num_splits_in_collection_dict = sum([len(splits) for splits in list(collection_dict.values())])
splits_in_collection_dict = set(list(chain.from_iterable(list(collection_dict.values()))))
if len(splits_in_collection_dict) != num_splits_in_collection_dict:
raise ConfigError("TablesForCollections::append: %d of the split or contig IDs appear more than once in\
your collections input. It is unclear to anvi'o how did you manage to do this, but we\
cannot go anywhere with this :/" % (num_splits_in_collection_dict - len(splits_in_collection_dict)))
database = db.DB(self.db_path, utils.get_required_version_for_db(self.db_path))
# how many clusters are defined in 'collection_dict'?
bin_names = list(collection_dict.keys())
# push information about this search result into serach_info table.
db_entries = tuple([collection_name, num_splits_in_collection_dict, len(bin_names), ','.join(bin_names)])
database._exec('''INSERT INTO %s VALUES (?,?,?,?)''' % t.collections_info_table_name, db_entries)
if not bins_info_dict:
colors = utils.get_random_colors_dict(bin_names)
for bin_name in bin_names:
bins_info_dict[bin_name] = {'html_color': colors[bin_name], 'source': 'UNKNOWN'}
# populate bins info table.
db_entries = [(self.next_id(t.collections_bins_info_table_name), collection_name, b, bins_info_dict[b]['source'], bins_info_dict[b]['html_color']) for b in bin_names]
database._exec_many('''INSERT INTO %s VALUES (?,?,?,?,?)''' % t.collections_bins_info_table_name, db_entries)
# populate splits table
db_entries = []
for bin_name in collection_dict:
for split_name in collection_dict[bin_name]:
db_entries.append(tuple([self.next_id(t.collections_splits_table_name), collection_name, split_name, bin_name]))
database._exec_many('''INSERT INTO %s VALUES (?,?,?,?)''' % t.collections_splits_table_name, db_entries)
num_splits = len(db_entries)
# FIXME: This function can be called to populate the contigs database (via anvi-populate-collections), or
# the profile database. when it is contigs database, the superclass Table has the self.splits_info variable
# set when it is initialized. however, the Table instance is missing self.splis when it is initialized with
# the profile database. hence some special controls for contigs db (note that collections_contigs_table is
# only populated in the contigs database):
if self.db_type == 'contigs':
splits_only_in_collection_dict = [c for c in splits_in_collection_dict if c not in self.splits_info]
splits_only_in_db = [c for c in self.splits_info if c not in splits_in_collection_dict]
if len(splits_only_in_collection_dict):
self.run.warning('%d of %d splits found in "%s" results are not in the database. This may be OK,\
but you must be the judge of it. If this is somewhat surprising, please use caution\
and make sure all is fine before going forward with you analysis.'\
% (len(splits_only_in_collection_dict), len(splits_in_collection_dict), collection_name))
if len(splits_only_in_db):
self.run.warning('%d of %d splits found in the database were missing from the "%s" results. If this\
does not make any sense, please make sure you know why before going any further.'\
% (len(splits_only_in_db), len(self.splits_info), collection_name))
# then populate contigs table.
db_entries = self.process_contigs(collection_name, collection_dict)
database._exec_many('''INSERT INTO %s VALUES (?,?,?,?)''' % t.collections_contigs_table_name, db_entries)
database.disconnect()
num_bins = len(bin_names)
num_bins_to_report = 50
if num_bins <= num_bins_to_report:
bins_to_report = bin_names
bin_report_msg = "Here is a full list of the bin names in this collection: {}.".format(",".join(bins_to_report))
else:
bins_to_report = bin_names[:num_bins_to_report]
bin_report_msg = "Here is a list of the first {} bin names in this collection: {}.".format(num_bins_to_report, ",".join(bins_to_report))
self.run.info('Collections', 'The collection "%s" that describes %s splits and %s bins has been successfully added to the\
database at "%s". %s' % (collection_name, pp(num_splits), pp(num_bins), self.db_path, bin_report_msg), mc='green')
def append(self,
collection_name,
collection_dict,
bins_info_dict={},
drop_collection=True):
utils.is_this_name_OK_for_database('collection name',
collection_name,
stringent=False)
for bin_name in collection_dict:
utils.is_this_name_OK_for_database('bin name',
bin_name,
stringent=False)
if bins_info_dict:
if set(collection_dict.keys()) - set(bins_info_dict.keys()):
raise ConfigError(
f"Bins in the collection dict do not match to the ones in the bins info dict. "
f"They do not have to be identical, but for each bin id, there must be a unique "
f"entry in the bins informaiton dict. There is something wrong with your input :/"
)
if drop_collection:
# remove any pre-existing information for 'collection_name'
self.delete(collection_name)
num_splits_in_collection_dict = sum(
[len(splits) for splits in list(collection_dict.values())])
splits_in_collection_dict = set(
list(chain.from_iterable(list(collection_dict.values()))))
if len(splits_in_collection_dict) != num_splits_in_collection_dict:
raise ConfigError(
f"TablesForCollections::append: {(num_splits_in_collection_dict - len(splits_in_collection_dict))} "
f"split names or contig IDs appear more than once in your input for this collection. This part of "
f"the code is unable to predict how you may have ended up here, but check your input file maybe? :/"
)
database = db.DB(self.db_path,
utils.get_required_version_for_db(self.db_path))
# how many clusters are defined in 'collection_dict'?
bin_names = list(collection_dict.keys())
if drop_collection:
db_entries = tuple([
collection_name, num_splits_in_collection_dict,
len(bin_names), ','.join(bin_names)
])
database._exec(
'''INSERT INTO %s VALUES (?,?,?,?)''' %
t.collections_info_table_name, db_entries)
if not bins_info_dict:
colors = utils.get_random_colors_dict(bin_names)
for bin_name in bin_names:
bins_info_dict[bin_name] = {
'html_color': colors[bin_name],
'source': 'UNKNOWN'
}
# populate bins info table.
db_entries = [(collection_name, b, bins_info_dict[b]['source'],
bins_info_dict[b]['html_color']) for b in bin_names]
database._exec_many(
'''INSERT INTO %s VALUES (?,?,?,?)''' %
t.collections_bins_info_table_name, db_entries)
# populate splits table
db_entries = []
for bin_name in collection_dict:
for split_name in collection_dict[bin_name]:
db_entries.append(
tuple([collection_name, split_name, bin_name]))
database._exec_many(
'''INSERT INTO %s VALUES (?,?,?)''' %
t.collections_splits_table_name, db_entries)
num_splits = len(db_entries)
# FIXME: This function can be called to populate the contigs database (via anvi-populate-collections), or
# the profile database. when it is contigs database, the superclass Table has the self.splits_info variable
# set when it is initialized. however, the Table instance is missing self.splis when it is initialized with
# the profile database. hence some special controls for contigs db (note that collections_contigs_table is
# only populated in the contigs database):
if self.db_type == 'contigs':
splits_only_in_collection_dict = [
c for c in splits_in_collection_dict
if c not in self.splits_info
]
splits_only_in_db = [
c for c in self.splits_info
if c not in splits_in_collection_dict
]
if len(splits_only_in_collection_dict):
self.run.warning(
f"{len(splits_only_in_collection_dict)} of {len(splits_in_collection_dict)} splits found in "
f"collection '{collection_name}' are not known to the contigs database. This may be OK, but "
f"you must be the judge of it. If this surprises you, please use caution and make sure all "
f"is fine before going forward with you analysis.")
if len(splits_only_in_db):
self.run.warning('%d of %d splits found in the database were missing from the "%s" results. If this '
'does not make any sense, please make sure you know why before going any further.'\
% (len(splits_only_in_db), len(self.splits_info), collection_name))
# then populate contigs table.
db_entries = self.process_contigs(collection_name, collection_dict)
database._exec_many(
'''INSERT INTO %s VALUES (?,?,?,?)''' %
t.collections_contigs_table_name, db_entries)
database.disconnect()
num_bins = len(bin_names)
num_bins_to_report = 50
if not drop_collection:
bins_to_report = bin_names
bin_report_msg = f"Here is a full list of the bin names added to this collection: {', '.join(bins_to_report)}."
elif num_bins <= num_bins_to_report:
bins_to_report = bin_names
bin_report_msg = f"Here is a full list of the bin names in this collection: {', '.join(bins_to_report)}."
else:
bins_to_report = bin_names[:num_bins_to_report]
bin_report_msg = f"Here is a list of the first {P('bin name', num_bins_to_report)} in this collection: {', '.join(bins_to_report)}."
if drop_collection:
self.run.info(
'Collections',
f"The collection '{collection_name}' that describes {P('split', num_splits)} in {P('bin', num_bins)} was successfully "
f"added to the to the database at '{self.db_path}'. {bin_report_msg}",
mc='green')
else:
self.run.info(
'Collections',
f"The existing collection '{collection_name}' updated and {P('split', num_splits)} in {P('bin', num_bins)} were successfully "
f"added to the to the database at '{self.db_path}'. {bin_report_msg}",
mc='green')