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Snakefile_noTemp
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from os.path import join
configfile: "config/config.yaml"
# Define variables for multiple values
GRAPH_IDS = config["graph_id"]
WALK_LENGTHS = config["walk_lengths"]
N_WALKS = config["n_walks"]
P_VALUES = config["p"]
Q_VALUES = config["q"]
PERPLEXITIES = config["perplexities"]
N_ITERS = config["n_iters"]
DIMENSIONS = config["dimensions"]
rule all:
input:
expand(join(config["graphDir"], "{graph_id}.gfa"), graph_id=GRAPH_IDS),
expand(join(config["linksDir"], "{graph_id}_links.json"), graph_id=GRAPH_IDS),
# Walks outputs
# expand(join(config["walkListsDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q_walks_vectorized.txt"),
# graph_id=GRAPH_IDS,
# walk_length=WALK_LENGTHS,
# n_walks=N_WALKS,
# p=P_VALUES,
# q=Q_VALUES),
# expand(join(config["walkDictsDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q_walks_oriented.json"),
# graph_id=GRAPH_IDS,
# walk_length=WALK_LENGTHS,
# n_walks=N_WALKS,
# p=P_VALUES,
# q=Q_VALUES),
# # # model embeddings
# expand(join(config["modelDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q{k}k_walks.model"),
# graph_id=GRAPH_IDS,
# walk_length=WALK_LENGTHS,
# n_walks=N_WALKS,
# p=P_VALUES,
# q=Q_VALUES,
# k=DIMENSIONS),
# expand(join(config["embeddingsDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q{k}k_walks.embeddings"),
# graph_id=GRAPH_IDS,
# walk_length=WALK_LENGTHS,
# n_walks=N_WALKS,
# p=P_VALUES,
# q=Q_VALUES,
# k=DIMENSIONS),
# expand(join(config["edgeEmbeddingsDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q{k}k_walks.edge_embeddings"),
# graph_id=GRAPH_IDS,
# walk_length=WALK_LENGTHS,
# n_walks=N_WALKS,
# p=P_VALUES,
# q=Q_VALUES,
# k=DIMENSIONS),
# # plotting embedding with t-SNE
# expand(join(config["plotsDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q{k}k_{perplexity}perp{n_iter}iter_embeddingPlot.png"),
# graph_id=GRAPH_IDS,
# walk_length=WALK_LENGTHS,
# n_walks=N_WALKS,
# p=P_VALUES,
# q=Q_VALUES,
# perplexity=PERPLEXITIES,
# n_iter=N_ITERS,
# k=DIMENSIONS),
# # # cluster dict
# # expand(join(config["clustersDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q{k}k_clusters.json"),
# # graph_id=GRAPH_IDS,
# # walk_length=WALK_LENGTHS,
# # n_walks=N_WALKS,
# # p=P_VALUES,
# # q=Q_VALUES,
# # k=DIMENSIONS),
# # # pairwise distances
# expand(join(config["distancesDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q{k}k_pairwiseDistances.csv"),
# graph_id=GRAPH_IDS,
# walk_length=WALK_LENGTHS,
# n_walks=N_WALKS,
# p=P_VALUES,
# q=Q_VALUES,
# k=DIMENSIONS),
# # # # # degree info for each node
# expand(join(config["degreeDir"], "{graph_id}_node_degrees.csv"),
# graph_id=GRAPH_IDS),
# # joining pairwise distances plus degree for each node
# expand(join(config["distDegDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q{k}k_distancesWithDegree.csv"),
# graph_id=GRAPH_IDS,
# walk_length=WALK_LENGTHS,
# n_walks=N_WALKS,
# p=P_VALUES,
# q=Q_VALUES,
# k=DIMENSIONS),
# # # summary stats on degree + pairwise distance
# # expand(join(config["distDegDir"], "{graph_id}_{walk_length}Lw{n_walks}Nw{p}p{q}q{k}k_stats.csv"),
# # graph_id=GRAPH_IDS,
# # walk_length=WALK_LENGTHS,
# # n_walks=N_WALKS,
# # p=P_VALUES,
# # q=Q_VALUES,
# # k=DIMENSIONS)
include:
"workflow/rules/copan_node2vec_pmglocal_noTemp.smk"