Fast pruning of arbitrary graphs.
Clone repository:
git clone https://github.com/fgvieira/prune_graph.git
and compile:
cargo build --release
To run the tests:
cargo test
./target/release/prune_graph --in input.tsv --out out.keep
or:
zcat input.tsv.gz | ./target/release/prune_graph > out.keep
To plot the graph (optional)
cat out.dot | dot -Tsvg > out.svg
If you want to get a full list of option, just run:
./target/release/prune_graph --help
As input, you need a TSV file (with or without header) with, at least, three columns. The first two columns must be the node names (defining an edge), and an additional column with the edge's weight (can be specified with --weight_field).
If you want to transform input data, you can use any CSV manipulation tool (e.g. Miller or CSVtk). For example, to use absolute values on column 5:
cat test/example.tsv | mlr --tsv --implicit-csv-header put '$5 = abs($5)' | ./target/release/prune_graph --header [...]
To filter edges, you can use option --weight-filter with any expression supported by fasteval. For example, to use column 7 as weight and only consider edges > 0.2:
cat test/example.tsv | ./target/release/prune_graph --weight-field "column_7" --weight-filter "column_7 > 0.2" --out out.keep
or, if also wanted to filter on column_3 > 1000:
cat test/example.tsv | ./target/release/prune_graph --weight-field "column_7" --weight-filter "column_3 > 1000 && column_7 > 0.2" --out out.keep
or, if you want to only use 0.1 < weight > 0.2:
cat test/example.tsv | ./target/release/prune_graph --weight-field "column_7" --weight-filter "column_3 > 1000 && (column_7 < 0.1 || column_7 > 0.2)" --out out.keep
The output will be a list of the remaining nodes after pruning. Optionally, you can also get a list of the nodes that were removed (--out-excl).