walks

Extracts the walks of a pangenome graph.

The walks command outputs a file with walks for an entire graph.

Usage

panct walks \
  --out PATH \
  --verbosity [CRITICAL|ERROR|WARNING|INFO|DEBUG|NOTSET] \
  GFAFILE

Examples

To create a .walk.gz and .walk.gz.tbi file adjacent to a GFA, just specify the path to the GFA.

panct walks tests/data/basic.gfa

You can also specify the output file path manually. If the output path does not have a .gz ending, an index will not be created automatically.

panct walks --out basic.walk tests/data/basic.gfa

All files used in these examples are described here.

Additional examples

Below is an additional example based on the HPRC .gfa format graph (not included in this repo but available here).

panct walks hprc-v1.1-mc-grch38.gfa

This may take some time. You can speed it up by allocating more memory and CPUs. On our system, we allocated 16 CPUs, 32 GB of RAM, and 7 hours of compute.

Warning

The walks command may store thousands of small files (totaling up to ~100 GB) in your system’s temporary directory. On some systems, this directory may not have the capacity for walks from the entire HPRC pangenome. So we recommend setting the $TMPDIR environment variable to a larger directory when calling the walks command.

TMPDIR=/scratch/$USER/job_$SLURM_JOBID panct walks hprc-v1.1-mc-grch38.gfa

Ideally, you would choose a directory that is optimized for I/O-intensive work. In this example, we are using node-local scratch space on UCSD’s TSCC or Expanse HPCs, for instance.

Detailed Usage

panct

panct: A collection of tools for working with pangenomes

panct [OPTIONS] COMMAND [ARGS]...

Options

-v, --version

Show the application’s version and exit.

Default:

False

--install-completion

Install completion for the current shell.

--show-completion

Show completion for the current shell, to copy it or customize the installation.

walks

Extract walks to a file

panct walks [OPTIONS] GRAPH

Options

-o, --out <output_file>

Name of output file

-v, --verbosity <verbosity>

The level of verbosity desired

Default:

<Verbosity.info: 'INFO'>

Options:

CRITICAL | ERROR | WARNING | INFO | DEBUG | NOTSET

Arguments

GRAPH

Required argument

Path to the .gfa file of a pangenome graph