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/gfautil.

$ gfautil
gfautil 0.2.0

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
    gfa-segment-id-conversion    Convert a GFA with string names to one with integer names, and back
    gfa2vcf                      Output a VCF for the given GFA, using the graph's ultrabubbles to identify areas of
                                 variation. (experimental!)
    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

GFA -> VCF

Find the ultrabubbles in the input GFA, then use those to identify variants. For each ultrabubble, the section covered by the bubble is extracted from each embedded path. Those sub-paths are then compared pairwise.

Currently the variant identification is mostly based on the nodes that make up each path, and only barely takes the sequences into account.

Outputs is in the VCF format, on stdout.

gfautil --gfa ./example.gfa variant

There's a setting to skip comparing a pair of paths if their orientations at the start and end of the bubble don't match:

gfautil --gfa ./example.gfa variant --no-inv

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