Rust gfautil

Command line tool for various operations on GFA and related files.

Usage

Install with cargo:

bash cargo install gfautil

Or clone and build it:

bash git clone https://github.com/chfi/rs-gfa-utils.git cd rs-gfa-utils cargo build --release

The compiled binary will be located at target/release/gfautils.

```bash $ gfautil --help gfautil 0.1.0

USAGE: gfautil --gfa

FLAGS: -h, --help Prints help information

-V, --version
        Prints version information

OPTIONS: -i, --gfa

SUBCOMMANDS: edge-count gaf2paf Convert a file of GAF records into PAF records help Prints this message or the help of the given subcommand(s) subgraph Generate a subgraph of the input GFA ```

GAF -> PAF

Given a GAF file, and the GFA used to create it, output a PAF file derived from the GAF records. For every path segment in each GAF record, a corresponding PAF record is produced.

Convert example.gaf, via example.gfa, with output on stdout:

bash gfautil --gfa ./example.gfa gaf2paf --gaf ./example.gaf

Save output to out.paf:

bash gfautil --gfa ./example.gfa gaf2paf --gaf ./example.gaf -o out.paf

Subgraph

Return a subgraph of the given GFA. Provide either a list of segment names, or a list of path names. If segment names are provided, the resulting subgraph will include the lines that contain at least one of those segments. If path names are provided, the segments in the given paths are used instead.

bash gfautil --gfa example.gfa subgraph segments --names s1 s2 s3

bash cat names.txt s1 s2 s3 gfautil --gfa example.gfa subgraph segments --file names.txt

bash gfautil --gfa example.gfa subgraph paths --names p1 p2