def test_additional_edges():
import convert_networks_to_graphml
import networkx as nx
import constants_network as CONST
logger.debug(
"Exporting ion identity molecular network with ALL nodes (NO collapsing)"
)
convert_networks_to_graphml.create_graphml(
"reference_data/IIN/edges.tsv",
"reference_data/IIN/cluster_summary.tsv",
"reference_data/IIN/library_matches.tsv",
"reference_data/IIN/library_matches.tsv",
"reference_data/IIN/additional_edges", "iin.graphml")
logger.info("Reading graph")
G = nx.read_graphml("iin.graphml")
logger.info("Number of nodes in IIMN graph: " + str(len(G.nodes())))
logger.info("Number of edges in IIMN graph: " + str(len(G.edges())))
listy = G.get_edge_data('7347', '9043')
logger.info("edge info:" + str(listy))
mass_difference = float(listy[CONST.EDGE.ION_TYPE]["mass_difference"])
#mass_difference = round(mass_difference, 4)
# safely compare floating point numbers
assert (numpy.isclose(mass_difference, 3.0051))
def test_additional_edges():
import convert_networks_to_graphml
convert_networks_to_graphml.create_graphml(
"reference_data/IIN/edges.tsv",
"reference_data/IIN/cluster_summary.tsv",
"reference_data/IIN/library_matches.tsv",
"reference_data/IIN/library_matches.tsv",
"reference_data/IIN/additional_edges", "iin.graphml")
def test_additional_edges():
import convert_networks_to_graphml
import networkx as nx
import unittest
convert_networks_to_graphml.create_graphml("reference_data/IIN/edges.tsv",
"reference_data/IIN/cluster_summary.tsv",
"reference_data/IIN/library_matches.tsv",
"reference_data/IIN/library_matches.tsv",
"reference_data/IIN/additional_edges",
"iin.graphml")
G = nx.read_graphml("iin.graphml")
listy = G.get_edge_data('7347','9043')
mass_difference = float(listy[0]["mass_difference"])
mass_difference = round(mass_difference, 4)
assert(mass_difference == 3.0051)
def test_collapse_ion_identity_networks():
import convert_networks_to_graphml
import networkx as nx
logger.info("Exporting ion identity molecular network with collapsed nodes")
convert_networks_to_graphml.create_graphml("reference_data/IIN/edges.tsv",
"reference_data/IIN/cluster_summary.tsv",
"reference_data/IIN/library_matches.tsv",
"reference_data/IIN/library_matches.tsv",
"reference_data/IIN/additional_edges",
"iin.graphml", collapse_ion_edges=True)
logger.info("Reading graph")
G = nx.read_graphml("iin.graphml")
logger.info("Number of nodes in collapsed IIMN graph: " + str(len(G.nodes())))
logger.info("Number of edges in collapsed IIMN graph: " + str(len(G.edges())))
# TODO: add test values
assert (len(G.nodes()) < 1140)