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author | S. Solomon Darnell | 2025-03-28 21:52:21 -0500 |
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committer | S. Solomon Darnell | 2025-03-28 21:52:21 -0500 |
commit | 4a52a71956a8d46fcb7294ac71734504bb09bcc2 (patch) | |
tree | ee3dc5af3b6313e921cd920906356f5d4febc4ed /.venv/lib/python3.12/site-packages/networkx/readwrite/p2g.py | |
parent | cc961e04ba734dd72309fb548a2f97d67d578813 (diff) | |
download | gn-ai-master.tar.gz |
Diffstat (limited to '.venv/lib/python3.12/site-packages/networkx/readwrite/p2g.py')
-rw-r--r-- | .venv/lib/python3.12/site-packages/networkx/readwrite/p2g.py | 105 |
1 files changed, 105 insertions, 0 deletions
diff --git a/.venv/lib/python3.12/site-packages/networkx/readwrite/p2g.py b/.venv/lib/python3.12/site-packages/networkx/readwrite/p2g.py new file mode 100644 index 00000000..804adb23 --- /dev/null +++ b/.venv/lib/python3.12/site-packages/networkx/readwrite/p2g.py @@ -0,0 +1,105 @@ +""" +This module provides the following: read and write of p2g format +used in metabolic pathway studies. + +See https://web.archive.org/web/20080626113807/http://www.cs.purdue.edu/homes/koyuturk/pathway/ for a description. + +The summary is included here: + +A file that describes a uniquely labeled graph (with extension ".gr") +format looks like the following: + + +name +3 4 +a +1 2 +b + +c +0 2 + +"name" is simply a description of what the graph corresponds to. The +second line displays the number of nodes and number of edges, +respectively. This sample graph contains three nodes labeled "a", "b", +and "c". The rest of the graph contains two lines for each node. The +first line for a node contains the node label. After the declaration +of the node label, the out-edges of that node in the graph are +provided. For instance, "a" is linked to nodes 1 and 2, which are +labeled "b" and "c", while the node labeled "b" has no outgoing +edges. Observe that node labeled "c" has an outgoing edge to +itself. Indeed, self-loops are allowed. Node index starts from 0. + +""" + +import networkx as nx +from networkx.utils import open_file + + +@open_file(1, mode="w") +def write_p2g(G, path, encoding="utf-8"): + """Write NetworkX graph in p2g format. + + Notes + ----- + This format is meant to be used with directed graphs with + possible self loops. + """ + path.write((f"{G.name}\n").encode(encoding)) + path.write((f"{G.order()} {G.size()}\n").encode(encoding)) + nodes = list(G) + # make dictionary mapping nodes to integers + nodenumber = dict(zip(nodes, range(len(nodes)))) + for n in nodes: + path.write((f"{n}\n").encode(encoding)) + for nbr in G.neighbors(n): + path.write((f"{nodenumber[nbr]} ").encode(encoding)) + path.write("\n".encode(encoding)) + + +@open_file(0, mode="r") +@nx._dispatchable(graphs=None, returns_graph=True) +def read_p2g(path, encoding="utf-8"): + """Read graph in p2g format from path. + + Returns + ------- + MultiDiGraph + + Notes + ----- + If you want a DiGraph (with no self loops allowed and no edge data) + use D=nx.DiGraph(read_p2g(path)) + """ + lines = (line.decode(encoding) for line in path) + G = parse_p2g(lines) + return G + + +@nx._dispatchable(graphs=None, returns_graph=True) +def parse_p2g(lines): + """Parse p2g format graph from string or iterable. + + Returns + ------- + MultiDiGraph + """ + description = next(lines).strip() + # are multiedges (parallel edges) allowed? + G = nx.MultiDiGraph(name=description, selfloops=True) + nnodes, nedges = map(int, next(lines).split()) + nodelabel = {} + nbrs = {} + # loop over the nodes keeping track of node labels and out neighbors + # defer adding edges until all node labels are known + for i in range(nnodes): + n = next(lines).strip() + nodelabel[i] = n + G.add_node(n) + nbrs[n] = map(int, next(lines).split()) + # now we know all of the node labels so we can add the edges + # with the correct labels + for n in G: + for nbr in nbrs[n]: + G.add_edge(n, nodelabel[nbr]) + return G |