# make_prg
A tool to create and update PRGs for input to [Pandora][pandora] and [Gramtools][gramtools] from a set of
Multiple Sequence Alignments.
[](https://codecov.io/github/iqbal-lab-org/make_prg)
[](https://opensource.org/licenses/MIT)
[](https://github.com/psf/black)
# Support
We fully support `make_prg` on `linux` with `python` versions `3.8`-`3.11`. For other operating systems, `make_prg`
can be run through containers.
[TOC]: #
## Table of Contents
- [Install](#install)
- [No installation needed - precompiled portable binary](#no-installation-needed---precompiled-portable-binary)
- [pip](#pip)
- [conda](#conda)
- [Container](#container)
- [Running on a sample example](#running-on-a-sample-example)
- [Usage](#usage)
## Install
### No installation needed - precompiled portable binary
You can use `make_prg` with no installation at all by simply downloading the precompiled binary, and running it.
In this binary, all libraries are linked statically. Compilation is done using [PyInstaller](https://github.com/pyinstaller/pyinstaller).
#### Requirements
`GLIBC >= 2.29` (present on `Ubuntu >= 19.04`, `Debian >= 11`, `CentOS >= 9`, etc);
#### Download
```
wget https://github.com/iqbal-lab-org/make_prg/releases/download/0.5.0/make_prg_0.5.0
```
#### Run
```
chmod +x make_prg_0.5.0
./make_prg_0.5.0 -h
```
### pip
**Requirements**: `python>=3.8,<=3.11`
```sh
pip install make_prg
```
### conda
```sh
conda install -c bioconda make_prg
```
### Container
Docker images are hosted at [quay.io].
#### `singularity`
Prerequisite: [`singularity`][singularity]
```sh
URI="docker://quay.io/iqballab/make_prg"
singularity exec "$URI" make_prg --help
```
The above will use the latest version. If you want to specify a version then use a
[tag][quay.io] (or commit) like so.
```sh
VERSION="0.5.0"
URI="docker://quay.io/iqballab/make_prg:${VERSION}"
```
#### `docker`
[](https://quay.io/repository/iqballab/make_prg)
Prerequisite: [`docker`][docker]
```sh
docker pull quay.io/iqballab/make_prg
docker run quay.io/iqballab/make_prg --help
```
You can find all the available tags on the [quay.io repository][quay.io].
## Running on a sample example
To see how to input files to both `make_prg from_msa` and `make_prg update`, and the outputs
they create on a sample example, see [sample example](sample_example).
## Usage
```
$ make_prg --help
usage: make_prg <subcommand> <options>
Subcommand entrypoint
options:
-h, --help show this help message and exit
-V, --version show program's version number and exit
Available subcommands:
from_msa Make PRG from multiple sequence alignment
update Update PRGs given new sequences.
```
#### `from_msa`
```
$ make_prg from_msa --help
usage: make_prg from_msa
options:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Multiple sequence alignment file or a directory containing such files
-s SUFFIX, --suffix SUFFIX
If the input parameter (-i, --input) is a directory, then filter for files with this suffix. If this parameter is not given, all files in the input directory is considered.
-o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
Prefix for the output files
-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_TYPE, --output-type OUTPUT_TYPE
p: PRG, b: Binary, g: GFA, a: All. Combinations are allowed i.e., gb: GFA and Binary. Default: a
-F, --force Force overwrite previous output
-t THREADS, --threads THREADS
Number of threads. 0 will use all available. Default: 1
-v, --verbose Increase output verbosity (-v for debug, -vv for trace - trace is for developers only)
--log LOG Path to write log to. Default is stderr
```
#### `update`
```
$ make_prg update --help
usage: make_prg update
options:
-h, --help show this help message and exit
-u UPDATE_DS, --update-DS UPDATE_DS
Filepath to the update data structures (a *.update_DS.zip file created from make_prg from_msa or update)
-o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
Prefix for the output files
-d DENOVO_PATHS, --denovo-paths DENOVO_PATHS
Filepath containing denovo sequences. Should point to a denovo_paths.txt file
-D LONG_DELETION_THRESHOLD, --deletion-threshold LONG_DELETION_THRESHOLD
Ignores long deletions of the given size or longer. If long deletions should not be ignored, put a large value. Default: 10
-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
-F, --force Force overwrite previous output
-t THREADS, --threads THREADS
Number of threads. 0 will use all available. Default: 1
-v, --verbose Increase output verbosity (-v for debug, -vv for trace - trace is for developers only)
--log LOG Path to write log to. Default is stderr
```
[pandora]: https://github.com/rmcolq/pandora
[gramtools]: https://github.com/iqbal-lab-org/gramtools/
[docker]: https://docs.docker.com/v17.12/install/
[quay.io]: https://quay.io/repository/iqballab/make_prg
[singularity]: https://sylabs.io/guides/3.4/user-guide/quick_start.html#quick-installation-steps
Raw data
{
"_id": null,
"home_page": "https://github.com/iqbal-lab-org/make_prg",
"name": "make-prg",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.8,<=3.11",
"maintainer_email": "",
"keywords": "python,reference-graph,genome-graph,bioinformatics",
"author": "Michael Hall",
"author_email": "michael@mbh.sh",
"download_url": "https://files.pythonhosted.org/packages/4f/2e/dcaea80f51948d5b132200a2866b6feb44a687cee0e0967feb80ebda36c7/make_prg-0.5.0.tar.gz",
"platform": null,
"description": "# make_prg\n\nA tool to create and update PRGs for input to [Pandora][pandora] and [Gramtools][gramtools] from a set of \nMultiple Sequence Alignments.\n\n \n[](https://codecov.io/github/iqbal-lab-org/make_prg)\n[](https://opensource.org/licenses/MIT)\n[](https://github.com/psf/black)\n\n\n# Support\n\nWe fully support `make_prg` on `linux` with `python` versions `3.8`-`3.11`. For other operating systems, `make_prg`\ncan be run through containers.\n\n[TOC]: #\n\n## Table of Contents\n- [Install](#install)\n - [No installation needed - precompiled portable binary](#no-installation-needed---precompiled-portable-binary)\n - [pip](#pip)\n - [conda](#conda)\n - [Container](#container)\n- [Running on a sample example](#running-on-a-sample-example)\n- [Usage](#usage)\n\n## Install\n\n### No installation needed - precompiled portable binary\n\nYou can use `make_prg` with no installation at all by simply downloading the precompiled binary, and running it.\nIn this binary, all libraries are linked statically. Compilation is done using [PyInstaller](https://github.com/pyinstaller/pyinstaller).\n\n#### Requirements\n`GLIBC >= 2.29` (present on `Ubuntu >= 19.04`, `Debian >= 11`, `CentOS >= 9`, etc);\n\n#### Download\n```\nwget https://github.com/iqbal-lab-org/make_prg/releases/download/0.5.0/make_prg_0.5.0\n```\n\n#### Run\n```\nchmod +x make_prg_0.5.0\n./make_prg_0.5.0 -h\n```\n\n### pip\n\n**Requirements**: `python>=3.8,<=3.11`\n\n```sh\npip install make_prg\n```\n\n### conda\n\n```sh\nconda install -c bioconda make_prg\n```\n\n### Container\n\nDocker images are hosted at [quay.io].\n\n#### `singularity`\n\nPrerequisite: [`singularity`][singularity]\n\n```sh\nURI=\"docker://quay.io/iqballab/make_prg\"\nsingularity exec \"$URI\" make_prg --help\n```\n\nThe above will use the latest version. If you want to specify a version then use a\n[tag][quay.io] (or commit) like so.\n\n```sh\nVERSION=\"0.5.0\"\nURI=\"docker://quay.io/iqballab/make_prg:${VERSION}\"\n```\n\n#### `docker`\n\n[![Docker Repository on Quay](https://quay.io/repository/iqballab/make_prg/status \"Docker Repository on Quay\")](https://quay.io/repository/iqballab/make_prg)\n\nPrerequisite: [`docker`][docker]\n\n```sh\ndocker pull quay.io/iqballab/make_prg\ndocker run quay.io/iqballab/make_prg --help\n```\n\nYou can find all the available tags on the [quay.io repository][quay.io].\n\n## Running on a sample example\n\nTo see how to input files to both `make_prg from_msa` and `make_prg update`, and the outputs\nthey create on a sample example, see [sample example](sample_example).\n\n## Usage\n\n```\n$ make_prg --help\nusage: make_prg <subcommand> <options>\n\nSubcommand entrypoint\n\noptions:\n -h, --help show this help message and exit\n -V, --version show program's version number and exit\n\nAvailable subcommands:\n \n from_msa Make PRG from multiple sequence alignment\n update Update PRGs given new sequences.\n```\n\n#### `from_msa`\n\n```\n$ make_prg from_msa --help\nusage: make_prg from_msa\n\noptions:\n -h, --help show this help message and exit\n -i INPUT, --input INPUT\n Multiple sequence alignment file or a directory containing such files\n -s SUFFIX, --suffix SUFFIX\n If the input parameter (-i, --input) is a directory, then filter for files with this suffix. If this parameter is not given, all files in the input directory is considered.\n -o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX\n Prefix for the output files\n -f ALIGNMENT_FORMAT, --alignment-format ALIGNMENT_FORMAT\n Alignment format of MSA, must be a biopython AlignIO input alignment_format. See http://biopython.org/wiki/AlignIO. Default: fasta\n -N MAX_NESTING, --max-nesting MAX_NESTING\n Maximum number of levels to use for nesting. Default: 5\n -L MIN_MATCH_LENGTH, --min-match-length MIN_MATCH_LENGTH\n Minimum number of consecutive characters which must be identical for a match. Default: 7\n -O OUTPUT_TYPE, --output-type OUTPUT_TYPE\n p: PRG, b: Binary, g: GFA, a: All. Combinations are allowed i.e., gb: GFA and Binary. Default: a\n -F, --force Force overwrite previous output\n -t THREADS, --threads THREADS\n Number of threads. 0 will use all available. Default: 1\n -v, --verbose Increase output verbosity (-v for debug, -vv for trace - trace is for developers only)\n --log LOG Path to write log to. Default is stderr\n```\n\n#### `update`\n\n```\n$ make_prg update --help\nusage: make_prg update\n\noptions:\n -h, --help show this help message and exit\n -u UPDATE_DS, --update-DS UPDATE_DS\n Filepath to the update data structures (a *.update_DS.zip file created from make_prg from_msa or update)\n -o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX\n Prefix for the output files\n -d DENOVO_PATHS, --denovo-paths DENOVO_PATHS\n Filepath containing denovo sequences. Should point to a denovo_paths.txt file\n -D LONG_DELETION_THRESHOLD, --deletion-threshold LONG_DELETION_THRESHOLD\n Ignores long deletions of the given size or longer. If long deletions should not be ignored, put a large value. Default: 10\n -O OUTPUT_TYPE, --output-type OUTPUT_TYPE\n p: PRG, b: Binary, g: GFA, a: All. Combinations are allowed i.e., gb: GFA and Binary. Default: a\n -F, --force Force overwrite previous output\n -t THREADS, --threads THREADS\n Number of threads. 0 will use all available. Default: 1\n -v, --verbose Increase output verbosity (-v for debug, -vv for trace - trace is for developers only)\n --log LOG Path to write log to. Default is stderr\n```\n\n[pandora]: https://github.com/rmcolq/pandora\n[gramtools]: https://github.com/iqbal-lab-org/gramtools/\n[docker]: https://docs.docker.com/v17.12/install/\n[quay.io]: https://quay.io/repository/iqballab/make_prg\n[singularity]: https://sylabs.io/guides/3.4/user-guide/quick_start.html#quick-installation-steps\n\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "Code to create a PRG from a Multiple Sequence Alignment file",
"version": "0.5.0",
"project_urls": {
"Documentation": "https://github.com/iqbal-lab-org/make_prg",
"Homepage": "https://github.com/iqbal-lab-org/make_prg",
"Repository": "https://github.com/iqbal-lab-org/make_prg"
},
"split_keywords": [
"python",
"reference-graph",
"genome-graph",
"bioinformatics"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "e6f4d2fdc19f4069bff7e2ad3b6258cdd3293e34e1f1b4e56dc1b8a3f98a0304",
"md5": "a680a5147097c6b4f805eb08a3039f1b",
"sha256": "925252978f662c7e6918065ea4d4f2beb8956bb305505e5f6ba77a5e239c1400"
},
"downloads": -1,
"filename": "make_prg-0.5.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "a680a5147097c6b4f805eb08a3039f1b",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8,<=3.11",
"size": 15887202,
"upload_time": "2023-07-20T10:08:58",
"upload_time_iso_8601": "2023-07-20T10:08:58.153385Z",
"url": "https://files.pythonhosted.org/packages/e6/f4/d2fdc19f4069bff7e2ad3b6258cdd3293e34e1f1b4e56dc1b8a3f98a0304/make_prg-0.5.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "4f2edcaea80f51948d5b132200a2866b6feb44a687cee0e0967feb80ebda36c7",
"md5": "bd370c981cb910cee42381af3298d710",
"sha256": "2cbc2cfdd426714b17126f04cf4031198839ab3c73c41ccfdcfca9ac0d950866"
},
"downloads": -1,
"filename": "make_prg-0.5.0.tar.gz",
"has_sig": false,
"md5_digest": "bd370c981cb910cee42381af3298d710",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8,<=3.11",
"size": 15801476,
"upload_time": "2023-07-20T10:09:01",
"upload_time_iso_8601": "2023-07-20T10:09:01.071464Z",
"url": "https://files.pythonhosted.org/packages/4f/2e/dcaea80f51948d5b132200a2866b6feb44a687cee0e0967feb80ebda36c7/make_prg-0.5.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-07-20 10:09:01",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "iqbal-lab-org",
"github_project": "make_prg",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "make-prg"
}
JSON
