def populate_misc_data_tables(self):
self.run.info_single("Additional data and layer orders...", nl_before=1, nl_after=1, mc="blue")
essential_fields = [f for f in self.atomic_data_fields if constants.IS_ESSENTIAL_FIELD(f)]
# initialize views.
args = argparse.Namespace(profile_db = self.merged_profile_db_path)
profile_db_super = dbops.ProfileSuperclass(args)
profile_db_super.load_views(omit_parent_column=True)
# figure out layer orders dictionary
layer_orders_data_dict = {}
failed_attempts = []
self.progress.new('Working on layer orders')
for essential_field in essential_fields:
self.progress.update('recovering order for "%s"' % (essential_field))
try:
data_value = clustering.get_newick_tree_data_for_dict(profile_db_super.views[essential_field]['dict'],
distance=self.distance,
linkage=self.linkage,
transpose=True)
layer_orders_data_dict[essential_field] = {'data_value': data_value, 'data_type': 'newick'}
except:
failed_attempts.append(essential_field)
self.progress.end()
if not len(layer_orders_data_dict):
self.run.warning("This may or may not be important: anvi'o attempted to generate orders for your\
samples based on the view data, however, it failed :/")
return
if len(failed_attempts):
self.run.warning("While anvi'o was trying to generate clusterings of samples based on view data\
available in the merged profile, clustering of some of the essential data\
failed. It is likely not a very big deal, but you shall be the judge of it.\
Anvi'o now proceeds to store layers order information for those view items\
the clustering in fact worked. Here is the list of stuff that failed: '%s'"\
% (', '.join(failed_attempts)))
# add the layer orders quietly
TableForLayerOrders(args, r=terminal.Run(verbose=False)).add(layer_orders_data_dict)
self.run.warning(None, header="Layer orders added", lc='cyan')
for layer_order in layer_orders_data_dict:
self.run.info_single(layer_order, mc='cyan')
# done with layer orders. let's add our layer additional data and call it a day.
for data_group_name in self.layer_additional_data_dict:
args.target_data_group = data_group_name
TableForLayerAdditionalData(args, r=terminal.Run(verbose=False)).add(self.layer_additional_data_dict[data_group_name],
list(self.layer_additional_data_keys[data_group_name]))
self.run.warning(None, header="Data groups added", lc='cyan')
for data_group in self.layer_additional_data_dict:
self.run.info_single('%s (w/%d items)' % (data_group, len(self.layer_additional_data_keys[data_group])), mc='cyan')
def populate_layers_additional_data_and_layer_orders(self):
self.run.info_single("Additional data and layer orders...", nl_before=1, nl_after=1, mc="blue")
essential_fields = [f for f in self.atomic_data_fields if constants.IS_ESSENTIAL_FIELD(f)]
# initialize views.
args = argparse.Namespace(profile_db = self.merged_profile_db_path)
profile_db_super = dbops.ProfileSuperclass(args)
profile_db_super.load_views(omit_parent_column=True)
# figure out sample orders dictionary
layer_orders_data_dict = {}
failed_attempts = []
self.progress.new('Working on layer orders')
for essential_field in essential_fields:
self.progress.update('recovering order for "%s"' % (essential_field))
try:
data_value = clustering.get_newick_tree_data_for_dict(profile_db_super.views[essential_field]['dict'],
distance=self.distance,
linkage=self.linkage,
transpose=True)
layer_orders_data_dict[essential_field] = {'data_value': data_value, 'data_type': 'newick'}
except:
failed_attempts.append(essential_field)
self.progress.end()
if not len(layer_orders_data_dict):
self.run.warning("This may or may not be important: anvi'o attempted to generate orders for your\
samples based on the view data, however, it failed :/")
return
if len(failed_attempts):
self.run.warning("While anvi'o was trying to generate clusterings of samples based on view data\
available in the merged profile, clustering of some of the essential data\
failed. It is likely not a very big deal, but you shall be the judge of it.\
Anvi'o now proceeds to store layers order information for those view items\
the clustering in fact worked. Here is the list of stuff that failed: '%s'"\
% (', '.join(failed_attempts)))
self.progress.new('Working on layer additional data')
self.progress.update('...')
layer_additional_data_dict = {}
for sample_name in self.sample_ids_found_in_input_dbs:
layer_additional_data_dict[sample_name] = {}
# figure out num reads mapped per sample:
for sample_name in self.sample_ids_found_in_input_dbs:
layer_additional_data_dict[sample_name]['num_mapped_reads'] = self.total_reads_mapped_per_sample[sample_name]
self.progress.end()
TableForLayerOrders(args).add(layer_orders_data_dict)
TableForLayerAdditionalData(args).add(layer_additional_data_dict, ['num_mapped_reads'])
def generate_tree(self):
gene_clusters = set(request.forms.getall('gene_clusters[]'))
name = request.forms.get('name')
program = request.forms.get('program')
aligner = request.forms.get('aligner')
store_tree = request.forms.get('store_tree')
temp_fasta_file = filesnpaths.get_temp_file_path()
temp_tree_file = filesnpaths.get_temp_file_path()
tree_text = None
try:
self.interactive.write_sequences_in_gene_clusters_for_phylogenomics(
gene_cluster_names=gene_clusters,
output_file_path=temp_fasta_file,
align_with=aligner)
drivers.driver_modules['phylogeny'][program]().run_command(
temp_fasta_file, temp_tree_file)
tree_text = open(temp_tree_file, 'rb').read().decode()
if store_tree:
TableForLayerOrders(self.interactive.args).add(
{name: {
'data_type': 'newick',
'data_value': tree_text
}})
# TO DO: instead of injecting new newick tree, we can use TableForLayerOrders.get()
self.interactive.layers_order_data_dict[name] = {
'newick': tree_text,
'basic': None
}
except Exception as e:
message = str(e.clear_text()) if 'clear_text' in dir(e) else str(e)
return json.dumps({'status': 1, 'message': message})
return json.dumps({'status': 0, 'tree': tree_text})