Prune Graph

Fast pruning of arbitrary graphs.

Instalation

Clone repository:

git clone https://github.com/fgvieira/prune_graph.git

and compile:

cargo build --release

To run the tests:

cargo test

Usage

./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

Input data

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).

Transform input data

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 [...]

Filter edges

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

Output

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).