Command line tool for various operations on GFA and related files.
Install with cargo:
cargo install gfautilOr clone and build it:
git clone https://github.com/chfi/rs-gfa-utils.git
cd rs-gfa-utils
cargo build --releaseThe compiled binary will be located at target/release/gfautil.
$ gfautil
gfautil 0.3.2
USAGE:
gfautil [FLAGS] [OPTIONS] -i <input GFA file> <SUBCOMMAND>
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 <input GFA file>
-t, --threads <threads> The number of threads to use when applicable. If omitted, Rayon's default will be used,
based on the RAYON_NUM_THREADS 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.
subgraph Generate a subgraph of the input GFA
ultrabubblesGiven 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 -i ./example.gfa gaf2paf --gaf ./example.gafSave output to out.paf:
gfautil -i ./example.gfa gaf2paf --gaf ./example.gaf -o out.pafFind 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.
gfautil -i ./example.gfa gfa2vcfThere'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 -i ./example.gfa gfa2vcf --no-invLoading the list of ultrabubbles from a file:
gfautil -i ./example.gfa gfa2vcf -u example.ultrabubblesGiven the name of a path in the input GFA to use as reference,
identify SNPs among all other paths, using either a list of
ultrabubbles constructed using the gfautil ultrabubbles command, or
a list of SNP positions.
Outputs a tab-delimited list in the format:
<query-path-name>\t<reference base>\t<reference pos>\t<query base>\t<query pos>
SNP positions can be provided as a list in the arguments to gfautil:
gfautil --debug -t 8 -i ./example.gfa snps --ref "reference path name" --snps 1234 5677 1> example.gfa.snpsSNP positions can also be provided as a file, with one position per line:
gfautil --debug -t 8 -i ./example.gfa snps --ref "reference path name" --snps-file ./positions.txt 1> example.gfa.snpsUsing ultrabubbles from a file:
gfautil -i ./example.gfa snps --ref the_path -u example.bubblesReturn 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 -i example.gfa subgraph segments --names s1 s2 s3cat names.txt
s1
s2
s3
gfautil -i example.gfa subgraph segments --file names.txtgfautil -i example.gfa subgraph paths --names p1 p2