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Add logging to universe export
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ddomingof committed Apr 25, 2019
1 parent 94e57a0 commit 8ca733f
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2 changes: 2 additions & 0 deletions src/pathme/cli.py
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@
from pybel.dsl import ComplexAbundance
from pybel.struct.mutation import collapse_to_genes, collapse_all_variants
from pybel_tools.analysis.spia import bel_to_spia_matrices, spia_matrices_to_excel
from pybel.struct.summary import count_functions
from tqdm import tqdm

import networkx as nx
Expand Down Expand Up @@ -405,6 +406,7 @@ def universe(kegg_path, reactome_path, wikipathways_path, output, no_flatten, no

click.echo(f"Export BEL graph to: {os.path.join(output, 'pathme_universe_bel_graph.bel.pickle')}")
click.echo(universe_graph.summary_str())
click.echo(count_functions(universe_graph))

to_pickle(universe_graph, os.path.join(output, "pathme_universe_bel_graph.bel.pickle"))

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