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/gfautil.

```bash $ gfautil gfautil 0.3.1

USAGE: gfautil [FLAGS] [OPTIONS] -i

FLAGS: --debug Show debug messages -h, --help Prints help information --info Show info messages --quiet Show no messages -V, --version Prints version information

OPTIONS: -i -t, --threads The number of threads to use when applicable. If omitted, Rayon's default will be used, based on the RAYONNUMTHREADS environment variable, or the number of logical CPUs

SUBCOMMANDS: edge-count gaf2paf Convert a file of GAF records into PAF records gfa2vcf Output a VCF for the given GFA, using the graph's ultrabubbles to identify areas of variation help Prints this message or the help of the given subcommand(s) id-convert Convert a GFA with string names to one with integer names, and back snps Given a reference path from the GFA, by name, find and report the SNPs for all other paths compared to the reference. Uses the graph's ultrabubbles to identify areas of variation subgraph Generate a subgraph of the input GFA ultrabubbles ```

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 -i ./example.gfa gaf2paf --gaf ./example.gaf

Save output to out.paf:

bash gfautil -i ./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.

The -u option can be used to load the ultrabubbles from a file (output by the ultrabubbles command) instead of computing them.

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.

bash gfautil -i ./example.gfa gfa2vcf

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:

bash gfautil -i ./example.gfa gfa2vcf --no-inv

Loading the list of ultrabubbles from a file: bash gfautil -i ./example.gfa gfa2vcf -u example.ultrabubbles

Identify SNPs in GFA against reference path

Given the name of a path in the input GFA to use as reference, uses the GFA's ultrabubbles to identify SNPs among all other paths. Outputs a tab-delimited list in the format:

<query-path-name>\t<reference base>\t<reference pos>\t<query base>\t<query pos>

Just like the gfa2vcf command, you can also provide the ultrabubbles as a file using the -u option.

bash gfautil -i ./example.gfa snps --ref the_path

Loading the list of ultrabubbles from a file: bash gfautil -i ./example.gfa snps --ref the_path -u example.bubbles

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

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

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