def remove_neighborhood(context, input_path, output_path, name):
if input_path is None:
input_stream = ctxstream(sys.stdin)
else:
input_stream = open(input_path, 'r')
with input_stream:
graph = GraphReader(input_stream).network
try:
graph.neighborhoods.remove(name)
except KeyError:
click.secho("No neighborhood with name %r was found" % name,
err=True,
fg='yellow')
if output_path is None:
output_stream = ctxstream(sys.stdout)
else:
output_stream = open(output_path, 'w')
with output_stream:
GraphWriter(graph, output_stream)
def glycan_network(context, database_connection, hypothesis_identifier,
edge_strategy, output_path):
conn = DatabaseBoundOperation(database_connection)
hypothesis = get_by_name_or_id(conn, GlycanHypothesis,
hypothesis_identifier)
if output_path is None:
output_stream = ctxstream(sys.stdout)
else:
output_stream = open(output_path, 'wb')
with output_stream:
db = GlycanCompositionDiskBackedStructureDatabase(
database_connection, hypothesis.id)
glycans = list(db)
graph = CompositionGraph(glycans)
if edge_strategy == 'manhattan':
graph.create_edges(1)
else:
raise click.ClickException("Could not find edge strategy %r" %
(edge_strategy, ))
GraphWriter(graph, output_stream)
def add_prebuild_neighborhoods_to_network(context, input_path, output_path,
name):
if input_path is None:
input_stream = ctxstream(sys.stdin)
else:
input_stream = open(input_path, 'r')
with input_stream:
graph = GraphReader(input_stream).network
if name == 'n-glycan':
neighborhoods = make_n_glycan_neighborhoods()
else:
raise LookupError(name)
for n in neighborhoods:
graph.neighborhoods.add(n)
if output_path is None:
output_stream = ctxstream(sys.stdout)
else:
output_stream = open(output_path, 'w')
with output_stream:
GraphWriter(graph, output_stream)
def add_neighborhood_to_network(context, input_path, output_path, name,
range_rule, expression_rule, ratio_rule):
if input_path is None:
input_stream = ctxstream(sys.stdin)
else:
input_stream = open(input_path, 'r')
with input_stream:
graph = GraphReader(input_stream).network
if name in graph.neighborhoods:
click.secho(
"This network already has a neighborhood called %s, overwriting" %
name,
fg='yellow',
err=True)
rules = []
for rule in range_rule:
expr, lo, hi, req = rule
lo = int(lo)
hi = int(hi)
req = req.lower().strip() in ('true', 'yes', '1')
rules.append(CompositionRangeRule(expr, lo, hi, req))
for rule in expression_rule:
expr, req = rule
req = req.lower().strip() in ('true', 'yes', '1')
rules.append(CompositionExpressionRule(expr, req))
for rule in ratio_rule:
numer, denom, threshold, req = rule
threshold = float(threshold)
req = req.lower().strip() in ('true', 'yes', '1')
rules.append(CompositionRatioRule(numer, denom, threshold, req))
graph.neighborhoods.add(CompositionRuleClassifier(name, rules))
if output_path is None:
output_stream = ctxstream(sys.stdout)
else:
output_stream = open(output_path, 'w')
with output_stream:
GraphWriter(graph, output_stream)