Rust gfautil

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

Usage

Install with cargo:

cargo install gfautil

Or clone and build it:

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.

$ gfautil --help
gfautil 0.1.0

USAGE:
    gfautil --gfa <input GFA file> <SUBCOMMAND>

FLAGS:
    -h, --help
            Prints help information

    -V, --version
            Prints version information


OPTIONS:
    -i, --gfa <input GFA file>



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:

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

Save output to out.paf:

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.

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

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

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