make_prg

A tool to create a PRG for input to Pandora and Gramtools from a Multiple Sequence Alignment.

Install
- Conda
- Local
- Container
Usage
- CLI
- Nextflow
Input
Changing parameters

Install

Conda

Prerequisite: conda (and bioconda channel correctly set up)

conda install make_prg

Local

Requirements: python>=3

git clone https://github.com/rmcolq/make_prg.git
cd make_prg
python -m pip install .
make_prg --help

To additionally run the tests

python -m pip install nose hypothesis
nosetests tests/

This installs the CLI tool make_prg. The nextflow script make_prg_nexflow.nf assumes that make_prg is installed.

Container

Containers for this tool are hosted on quay.io.

An example, of running it in a Singularity container would be

tag="latest"
URI="docker://quay.io/iqballab/make_prg:${tag}"
singularity exec "$URI" make_prg --help

A list of the valid tags can be found here.

Usage

CLI

$ make_prg --help
usage: make_prg <subcommand> <options>

Subcommand entrypoint

optional arguments:
  -h, --help     show this help message and exit
  -V, --version  show program's version number and exit
  -v, --verbose  Run with high verbosity (debug level logging)

Available subcommands:

    from_msa     Make PRG from multiple sequence alignment

`from_msa`

$ make_prg from_msa --help
usage: make_prg from_msa [options] <MSA input file>

positional arguments:
  MSA                   Input file: a multiple sequence alignment

optional arguments:
  -h, --help            show this help message and exit
  -f ALIGNMENT_FORMAT, --alignment_format ALIGNMENT_FORMAT
                        Alignment format of MSA, must be a biopython AlignIO input alignment_format. See http://biopython.org/wiki/AlignIO. Default: fasta
  -N MAX_NESTING, --max_nesting MAX_NESTING
                        Maximum number of levels to use for nesting. Default: 5
  -L MIN_MATCH_LENGTH, --min_match_length MIN_MATCH_LENGTH
                        Minimum number of consecutive characters which must be identical for a match. Default: 7
  -o OUTPUT_DIR, --outdir OUTPUT_DIR
                        Output directory. Default: .
  -n PRG_NAME, --prg_name PRG_NAME
                        Prg file name. Default: MSA file name
  -S SEQID, --seqid SEQID
                        Sequence identifier to use for the output sequence/PRG. Default is the file name
  --no_overwrite        Do not replace an existing prg file
  -O OUTPUT_TYPE, --output-type OUTPUT_TYPE
                        p: PRG, b: Binary, g: GFA, a: All. Combinations are allowed i.e., gb: GFA and Binary. Default: a
  --log LOG             Path to write log to. Default is stderr

Nextflow

Requirements: Nextflow

    Usage: nextflow run make_prg_nexflow.nf <arguments>

    Required arguments:
      --tsv_in  FILENAME  An index file of MSA to build PRGs of

    Optional arguments:

Input

Multiple Sequence Alignment files for genes/dna sequences for which we wantPRGs, and an tab-separated index of these in the form:

sample_id       infile
GC0000001   /absolute/path/to/GC0000001_na_aln.fa.gz
GC0000002   /absolute/path/to/GC0000002_na_aln.fa

Changing parameters

There are some parameters at the top of the nextflow file which could be changed but which I have not made command line parameters:

max_nesting             This is the maximum number depth of bubbles in PRG, setting to 1 will allow variants, \\
                        but no nesting
min_match_length        Controls graph complexity
alignment_format        Any format accepted by biopython's AlignIO
max_forks_make_prg      If working on a cluster which allows unlimited parallel jobs per user, this will be \\
                        used by nextflow to control maximum number of processes of this type that can run in \\
                        parallel.
max_forks_make_fasta

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

iqbal-lab-org / make_prg

Programming Languages