Pynteny
Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases - Published in JOSS (2023)
Science Score: 98.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
○Committers with academic emails
-
○Institutional organization owner
-
✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Scientific Fields
Repository
Query sequence database by HMMs arranged in predefined synteny structure
Basic Info
- Host: GitHub
- Owner: Robaina
- License: apache-2.0
- Language: Python
- Default Branch: main
- Homepage: https://robaina.github.io/Pynteny
- Size: 22.1 MB
Statistics
- Stars: 13
- Watchers: 1
- Forks: 1
- Open Issues: 2
- Releases: 4
Topics
Metadata Files
README.md
Synteny-aware hmm searches made easy
<!-- 
-->
1. :bulb: What is Pynteny?
Pynteny is Python tool to search for synteny blocks in (prokaryotic) sequence data through HMMs of the ORFs of interest and HMMER. By leveraging genomic context information, Pynteny can be employed to decrease the uncertainty of functional annotation of unlabelled sequence data due to the effect of paralogs. Pynteny can be accessed (i) through the command line or (ii) as a Python module.
Get more info in the documentation pages!
Check out the Pynteny paper in the Journal of Open Source Software!
2. :wrench: Setup
Install with conda:
- Pynteny requires Python 3.10. The easiest way to handle dependencies is by creating a dedicated conda environment:
bash
conda create -n pynteny -c bioconda -c conda-forge python=3.10 pynteny
conda activate pynteny
- Check that installation worked fine:
bash
(pynteny) pynteny --help
2.1. Installing on Windows
Pynteny is designed to run on Linux machines. However, it can be installed within the Windows Subsystem for Linux via conda.
2.2. Installing on MacOS with the latest ARM64 architecture
Pynteny doesn't currently support the latest ARM64 architecture of silicon processors (e.g. MacBook M1 and M2). If that is your case, you can install Pynteny using the workaround below (based on this post):
bash
CONDA_SUBDIR=osx-64 conda create -n pynteny_x86 python=3.10
conda activate pynteny_x86
conda config --env --set subdir osx-64
conda install -c bioconda pynteny
3. :rocket: Usage
Consider the following toy example of a syntenic block:
Here, we are interested in four genes which colocate according to the pattern above: genes A-C show consecutive locations in the positive strand, followed by three (untargeted) genes and followed by gene D, which is located in the negative strand.
Pynteny can be run either as a command line tool or as a Python module. To run pynteny in the command line, execute:
bash
conda activate pynteny
pynteny <subcommand> <options>
There are a number of available subcommands, which can be explored in the documentation pages.
For intance, to first download the PGAP's database containing a collection of profile HMMs as well as metadata:
bash
pynteny download --outdir data/hmms --unpack
Next, to build a labelled peptide database from DNA assembly data:
```bash pynteny build \ --data assembly.fa \ --outfile labelled_peptides.faa
```
Finally, to search the peptide database for the syntenic structure displayed above: >gene_A 0 >gene_B 0 >gene_C 3 <gene_D, and using the downloaded PGAP database:
bash
pynteny search \
--synteny_struc ">gene_A 0 >gene_B 0 >gene_C 3 <gene_D" \
--data labelled_peptides.faa \
--outdir results/ \
--gene_ids
4. :notebookwithdecorative_cover: Examples
Here are some Jupyter Notebooks with examples to show how Pynteny works:
You can find more notebooks in the examples directory. Find more info in the documentation.
5. :arrows_counterclockwise: Dependencies
Pynteny would not work without these awesome projects:
Thanks!
6. :octocat: Contributing
Contributions are always welcome! If you don't know where to start, you may find an interesting issue to work in here. Please, read our contribution guidelines first.
7. :black_nib: Citation
If you use this software, please cite it as below:
Semidán Robaina Estévez. (2023). Pynteny: synteny-aware hmm searches made easy (Version 1.0.0). Zenodo. https://zenodo.org/record/7696204
Owner
- Name: Semidán Robaina
- Login: Robaina
- Kind: user
- Location: Atlantic Ocean
- Company: Hapdera
- Website: https://www.linkedin.com/in/semidan-robaina/
- Twitter: srobainae
- Repositories: 12
- Profile: https://github.com/Robaina
Computational Biology | Data Science | Python Dev. | Ph.D. Systems Biology
JOSS Publication
Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases
Authors
Department of Microbiology. University of La Laguna. Spain.
Department of Microbiology. University of La Laguna. Spain.
Editor
Kevin M. Moerman
Tags
bioinformatics HMMER synteny HMMs sequencingCitation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Robaina Estévez"
given-names: "Semidán"
orcid: "https://orcid.org/0000-0003-0781-1677"
affiliation: "Department of Microbiology. University of La Laguna. Spain"
email: "srobaina@ull.edu.es"
title: "Pynteny: synteny-aware hmm searches made easy"
version: 1.0.0
doi: 10.5281/zenodo.7696204
date-released: 2023-03-03
url: "https://github.com/Robaina/Pynteny"
GitHub Events
Total
Last Year
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Semidán Robaina Estévez | s****a@g****m | 597 |
| Alex Batisse | a****e@h****m | 6 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 55
- Total pull requests: 33
- Average time to close issues: 20 days
- Average time to close pull requests: 1 day
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 0.62
- Average comments per pull request: 1.18
- Merged pull requests: 32
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Robaina (54)
- wchow (1)
Pull Request Authors
- Robaina (32)
- Batalex (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 20 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
pypi.org: pynteny
Multiple HMM - search via synteny structures in Python
- Homepage: http://github.com/robaina/Pynteny
- Documentation: https://pynteny.readthedocs.io/
- License: Creative Commons Attribution 4.0 International
-
Latest release: 0.0.2
published about 3 years ago
Rankings
Dependencies
- actions/checkout v3 composite
- actions/setup-python v4 composite
- actions/checkout v3 composite
- actions/setup-python v2 composite
- actions/checkout v3 composite
- actions/upload-artifact v1 composite
- openjournals/openjournals-draft-action master composite
- actions/checkout v3 composite
- codecov/codecov-action v3 composite
- conda-incubator/setup-miniconda v2 composite
- mcr.microsoft.com/devcontainers/miniconda 0-3 build
- mcr.microsoft.com/devcontainers/miniconda 0-3 build
- python ^3.8