def main():
parser = argparse.ArgumentParser(description='Creating GraphML')
parser.add_argument('input_pairs', help='input_pairs')
parser.add_argument('input_clusterinfosummary',
help='input_clusterinfosummary')
parser.add_argument('input_librarysearch', help='input_librarysearch')
parser.add_argument('output_graphml', help='output_graphml')
parser.add_argument('--input_analoglibrarysearch',
help='input_analoglibrarysearch')
parser.add_argument('--input_pairsfolder', help='input_pairsfolder')
args = parser.parse_args()
#Doing other filtering
G = molecular_network_filtering_library.loading_network(args.input_pairs,
hasHeaders=True)
molecular_network_filtering_library.add_clusterinfo_summary_to_graph(
G, args.input_clusterinfosummary)
molecular_network_filtering_library.add_library_search_results_to_graph(
G, args.input_librarysearch)
if args.input_pairsfolder is not None:
all_pairs_files = glob.glob(os.path.join(args.input_pairsfolder, "*"))
for additional_pairs_file in all_pairs_files:
print("Adding Additional Edges", additional_pairs_file)
molecular_network_filtering_library.add_additional_edges(
G, additional_pairs_file)
if args.input_analoglibrarysearch is not None:
molecular_network_filtering_library.add_library_search_results_to_graph(
G, args.input_librarysearch, annotation_prefix="Analog:")
nx.write_graphml(G, args.output_graphml, infer_numeric_types=True)
def main():
input_pairs = sys.argv[1]
#Doing other filtering
G = molecular_network_filtering_library.loading_network(input_pairs, hasHeaders=True)
molecular_network_filtering_library.add_clusterinfo_summary_to_graph(G, sys.argv[2])
molecular_network_filtering_library.add_library_search_results_to_graph(G, sys.argv[3])
nx.write_graphml(G, sys.argv[4])
def main():
input_pairs = sys.argv[1]
#Doing other filtering
G = molecular_network_filtering_library.loading_network(input_pairs,
hasHeaders=True)
molecular_network_filtering_library.add_clusterinfo_summary_to_graph(
G, sys.argv[2])
molecular_network_filtering_library.add_library_search_results_to_graph(
G, sys.argv[3])
nx.write_graphml(G, sys.argv[4], infer_numeric_types=True)
def create_graphml(input_pairs,
input_clusterinfosummary,
input_librarysearch,
input_analoglibrarysearch,
input_pairsfolder,
output_graphml,
collapse_ion_edges=False):
logger = logging_utils.get_logger(__name__)
# Doing other filtering
logger.debug("Creating network")
G = molecular_network_filtering_library.loading_network(input_pairs,
hasHeaders=True)
molecular_network_filtering_library.add_clusterinfo_summary_to_graph(
G, input_clusterinfosummary)
molecular_network_filtering_library.add_library_search_results_to_graph(
G, input_librarysearch)
# mark all nodes as feature or ion identity nodes (constants.NODE.TYPE_ATTRIBUTE)
logger.debug("Mark all node types")
ion_network_utils.mark_all_node_types(G)
# add analogs
if input_analoglibrarysearch is not None:
logger.debug("Add analog library search results")
molecular_network_filtering_library.add_library_search_results_to_graph(
G, input_analoglibrarysearch, annotation_prefix="Analog:")
# add additional edges - e.g. ion identity edges between different ion species of the same molecule
if input_pairsfolder is not None:
all_pairs_files = glob.glob(os.path.join(input_pairsfolder, "*"))
logger.debug("Adding additional edges from files: " +
str(len(all_pairs_files)))
for additional_pairs_file in all_pairs_files:
logger.debug("Adding Additional Edges from " +
str(additional_pairs_file))
molecular_network_filtering_library.add_additional_edges(
G, additional_pairs_file)
# collapse all ion identity networks, each into a single node
if collapse_ion_edges:
logger.debug("Collapsing additional edges of type: " +
CONST.EDGE.ION_TYPE)
try:
G = ion_network_utils.collapse_ion_networks(G)
except:
logger.debug("Failed collapsing")
pass
# export graphml
logger.info("Writing graphml: " + output_graphml)
nx.write_graphml(G, output_graphml, infer_numeric_types=True)
def main():
input_pairs = sys.argv[1]
#Doing other filtering
G = molecular_network_filtering_library.loading_network(input_pairs, hasHeaders=True)
molecular_network_filtering_library.add_clusterinfo_summary_to_graph(G, sys.argv[2])
molecular_network_filtering_library.add_library_search_results_to_graph(G, sys.argv[3])
folder_for_additional_pairs = sys.argv[4]
all_pairs_files = ming_fileio_library.list_files_in_dir(folder_for_additional_pairs)
for additional_pairs_file in all_pairs_files:
print("Adding Additional Edges", additional_pairs_file)
molecular_network_filtering_library.add_additional_edges(G, additional_pairs_file)
nx.write_graphml(G, sys.argv[5], infer_numeric_types=True)
def main():
input_pairs = sys.argv[1]
#Doing other filtering
G = molecular_network_filtering_library.loading_network(input_pairs,
hasHeaders=True)
molecular_network_filtering_library.add_clusterinfo_summary_to_graph(
G, sys.argv[2])
molecular_network_filtering_library.add_library_search_results_to_graph(
G, sys.argv[3])
folder_for_additional_pairs = sys.argv[4]
all_pairs_files = ming_fileio_library.list_files_in_dir(
folder_for_additional_pairs)
for additional_pairs_file in all_pairs_files:
print("Adding Additional Edges", additional_pairs_file)
molecular_network_filtering_library.add_additional_edges(
G, additional_pairs_file)
nx.write_graphml(G, sys.argv[5], infer_numeric_types=True)
def create_graphml(input_pairs, input_clusterinfosummary, input_librarysearch,
input_analoglibrarysearch, input_pairsfolder,
output_graphml):
#Doing other filtering
G = molecular_network_filtering_library.loading_network(input_pairs,
hasHeaders=True)
molecular_network_filtering_library.add_clusterinfo_summary_to_graph(
G, input_clusterinfosummary)
molecular_network_filtering_library.add_library_search_results_to_graph(
G, input_librarysearch)
if input_pairsfolder is not None:
all_pairs_files = glob.glob(os.path.join(input_pairsfolder, "*"))
for additional_pairs_file in all_pairs_files:
print("Adding Additional Edges", additional_pairs_file)
molecular_network_filtering_library.add_additional_edges(
G, additional_pairs_file)
if input_analoglibrarysearch is not None:
molecular_network_filtering_library.add_library_search_results_to_graph(
G, input_analoglibrarysearch, annotation_prefix="Analog:")
nx.write_graphml(G, output_graphml, infer_numeric_types=True)