.. image:: https://badge.fury.io/py/sequana-ribofinder.svg
:target: https://pypi.python.org/pypi/sequana_ribofinder
.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
:target: http://joss.theoj.org/papers/10.21105/joss.00352
:alt: JOSS (journal of open source software) DOI
.. image:: https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg
:target: https://github.com/sequana/ribofinder/actions/workflows/main.yml
.. image:: https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg
:target: https://pypi.python.org/pypi/sequana
:alt: Python 3.8 | 3.9 | 3.10
This is is the **ribofinder** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
:Overview: Simple parallele workflow to detect and report ribosomal content
:Input: FastQ files
:Output: HTML reports
:Status: production
:Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
Installation
~~~~~~~~~~~~
Using **pip** from Python, just install this package::
pip install sequana_ribofinder --upgrade
The **--upgrade** option is to make sure you'll get the latest version.
Usage
~~~~~
This pipeline scans input fastq.gz files found in the local
directory and identify the proportion of ribosomal content.
For help, please type::
sequana_ribofinder --help
The following command searches for input files in DATAPATH. Then, te user provide
a list of rRNA sequences in FastA format in *test.fasta*. This command creates a directory
called ribofinder/ where a snakemake pipeline can::
sequana_ribofinder --input-directory DATAPATH --rRNA-file test.fasta
You will then need to execute the pipeline::
cd ribofinder
sh ribofinder.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can
retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::
snakemake -s ribofinder.rules -c config.yaml --cores 4 --wrapper-prefix git+file:////home/user/sequana_wrappers
Or use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.
Requirements
~~~~~~~~~~~~
This pipelines requires the following executable(s):
- bowtie1 >= 1.3.0
- bedtools
- samtools
- bamtools
- pigz
.. image:: https://raw.githubusercontent.com/sequana/ribofinder/master/sequana_pipelines/ribofinder/dag.png
Details
~~~~~~~~~
This pipeline runs **ribofinder** in parallel on the input fastq files.
A brief sequana summary report is also produced.
You can start from the reference file and the GFF file. By default we search for the feature called
rRNA to be found in the GFF file::
sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff
If the default feature rRNA is not found, no error is raised for now. If you know the expected feature,
you can provide it though::
sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff --rRNA-feature gene_rRNA
If you have an existing or custom rRNA file, you can then use it as follows, in which case, no input reference is
required::
sequana_ribofinder --input-directory . --rRNA-file ribo.fasta
Rules and configuration details
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/ribofinder/master/sequana_pipelines/ribofinder/config.yaml>`_
to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
Changelog
~~~~~~~~~
========= ====================================================================
Version Description
========= ====================================================================
1.1.1 * hotfix for running on HPC (slurm)
1.1.0 * Uses click (refactoring of sequana_pipetools)
1.0.1 * add sequana_wrappers in the config/pipeline
1.0.0 * use graphviz apptainer and latest wrappers
0.13.0 * add final apptainers and update CI actions
0.12.0 * set singularity containers
0.11.1 * Fix config file (removing hard-coded path)
0.11.0 * Fix multiqc plot using same fix as in sequna_rnaseq pipelines
* add utility plot to check rate of ribosomal per sequence and also
the corresponding RPKM.
0.10.2 * Fix the bowtie1 rule (all samples were named bowtie1)
0.10.1 * add additional test and fix bug in pipeline (regression bug)
0.10.0 * Update to use sequana-wrappers. Remove multiqc. summary.html
is self-content
0.9.3 * fix logger
0.9.2 **First release.**
========= ====================================================================
Raw data
{
"_id": null,
"home_page": "https://github.com/sequana/ribofinder",
"name": "sequana-ribofinder",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.8,<4.0",
"maintainer_email": "",
"keywords": "snakemake,ribosomal,rRNA,sequana",
"author": "Sequana Team",
"author_email": "",
"download_url": "https://files.pythonhosted.org/packages/3a/00/5086b88360b00825f0529048fec06c618c47c94827e3ee5b8c73c1a4a012/sequana_ribofinder-1.1.1.tar.gz",
"platform": null,
"description": "\n.. image:: https://badge.fury.io/py/sequana-ribofinder.svg\n :target: https://pypi.python.org/pypi/sequana_ribofinder\n\n.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg\n :target: http://joss.theoj.org/papers/10.21105/joss.00352\n :alt: JOSS (journal of open source software) DOI\n\n.. image:: https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg\n :target: https://github.com/sequana/ribofinder/actions/workflows/main.yml\n\n.. image:: https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg\n :target: https://pypi.python.org/pypi/sequana\n :alt: Python 3.8 | 3.9 | 3.10\n\n\n\nThis is is the **ribofinder** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project\n\n:Overview: Simple parallele workflow to detect and report ribosomal content\n:Input: FastQ files\n:Output: HTML reports\n:Status: production\n:Citation: Cokelaer et al, (2017), \u2018Sequana\u2019: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352\n\n\nInstallation\n~~~~~~~~~~~~\n\nUsing **pip** from Python, just install this package::\n\n pip install sequana_ribofinder --upgrade\n\nThe **--upgrade** option is to make sure you'll get the latest version.\n\nUsage\n~~~~~\n\nThis pipeline scans input fastq.gz files found in the local\ndirectory and identify the proportion of ribosomal content.\n\nFor help, please type::\n\n sequana_ribofinder --help\n\nThe following command searches for input files in DATAPATH. Then, te user provide\na list of rRNA sequences in FastA format in *test.fasta*. This command creates a directory \ncalled ribofinder/ where a snakemake pipeline can::\n\n sequana_ribofinder --input-directory DATAPATH --rRNA-file test.fasta\n\nYou will then need to execute the pipeline::\n\n cd ribofinder\n sh ribofinder.sh # for a local run\n\nThis launch a snakemake pipeline. If you are familiar with snakemake, you can\nretrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::\n\n snakemake -s ribofinder.rules -c config.yaml --cores 4 --wrapper-prefix git+file:////home/user/sequana_wrappers\n\n\nOr use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s):\n\n- bowtie1 >= 1.3.0\n- bedtools\n- samtools\n- bamtools\n- pigz\n\n.. image:: https://raw.githubusercontent.com/sequana/ribofinder/master/sequana_pipelines/ribofinder/dag.png\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs **ribofinder** in parallel on the input fastq files. \nA brief sequana summary report is also produced.\n\nYou can start from the reference file and the GFF file. By default we search for the feature called \nrRNA to be found in the GFF file::\n\n sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff\n\nIf the default feature rRNA is not found, no error is raised for now. If you know the expected feature, \nyou can provide it though::\n\n sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff --rRNA-feature gene_rRNA\n\nIf you have an existing or custom rRNA file, you can then use it as follows, in which case, no input reference is\nrequired::\n\n sequana_ribofinder --input-directory . --rRNA-file ribo.fasta\n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/ribofinder/master/sequana_pipelines/ribofinder/config.yaml>`_\nto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. \n\nChangelog\n~~~~~~~~~\n\n========= ====================================================================\nVersion Description\n========= ====================================================================\n1.1.1 * hotfix for running on HPC (slurm)\n1.1.0 * Uses click (refactoring of sequana_pipetools)\n1.0.1 * add sequana_wrappers in the config/pipeline\n1.0.0 * use graphviz apptainer and latest wrappers\n0.13.0 * add final apptainers and update CI actions\n0.12.0 * set singularity containers\n0.11.1 * Fix config file (removing hard-coded path)\n0.11.0 * Fix multiqc plot using same fix as in sequna_rnaseq pipelines\n * add utility plot to check rate of ribosomal per sequence and also\n the corresponding RPKM.\n0.10.2 * Fix the bowtie1 rule (all samples were named bowtie1)\n0.10.1 * add additional test and fix bug in pipeline (regression bug)\n0.10.0 * Update to use sequana-wrappers. Remove multiqc. summary.html \n is self-content\n0.9.3 * fix logger\n0.9.2 **First release.**\n========= ====================================================================\n\n\n\n",
"bugtrack_url": null,
"license": "BSD-3",
"summary": "A multi-sample identification of ribosomal content",
"version": "1.1.1",
"project_urls": {
"Homepage": "https://github.com/sequana/ribofinder",
"Repository": "https://github.com/sequana/ribofinder"
},
"split_keywords": [
"snakemake",
"ribosomal",
"rrna",
"sequana"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "3741a1fd2d18dbff4feb972186963390b6383f18129b5dbd961f8498ddcd409b",
"md5": "5cf29315a1e229a0e1d499f8ee4a5d2a",
"sha256": "347f114d5688a98d05b1b7ee3e2e247ea59c77ed92a44bbbca5f39a0f512fbc7"
},
"downloads": -1,
"filename": "sequana_ribofinder-1.1.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "5cf29315a1e229a0e1d499f8ee4a5d2a",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8,<4.0",
"size": 33339,
"upload_time": "2023-12-05T09:50:42",
"upload_time_iso_8601": "2023-12-05T09:50:42.453451Z",
"url": "https://files.pythonhosted.org/packages/37/41/a1fd2d18dbff4feb972186963390b6383f18129b5dbd961f8498ddcd409b/sequana_ribofinder-1.1.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "3a005086b88360b00825f0529048fec06c618c47c94827e3ee5b8c73c1a4a012",
"md5": "0ea3bac42f50c862a05f4bfd48ebdcb1",
"sha256": "658938cfcd4d9dffadf5d243105e7dc27731985639e9b8dc12b7f3e0020ad9e0"
},
"downloads": -1,
"filename": "sequana_ribofinder-1.1.1.tar.gz",
"has_sig": false,
"md5_digest": "0ea3bac42f50c862a05f4bfd48ebdcb1",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8,<4.0",
"size": 33891,
"upload_time": "2023-12-05T09:50:57",
"upload_time_iso_8601": "2023-12-05T09:50:57.419167Z",
"url": "https://files.pythonhosted.org/packages/3a/00/5086b88360b00825f0529048fec06c618c47c94827e3ee5b8c73c1a4a012/sequana_ribofinder-1.1.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-12-05 09:50:57",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "sequana",
"github_project": "ribofinder",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "sequana-ribofinder"
}
JSON
