abstar
VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
9 of 15 committers (60.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.4%) to scientific vocabulary
Repository
VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
Basic Info
Statistics
- Stars: 42
- Watchers: 6
- Forks: 16
- Open Issues: 5
- Releases: 51
Metadata Files
README.md
abstar
VDJ assignment and antibody sequence annotation. Scalable from a single sequence to billions of sequences.
- Source code: github.com/brineylab/abstar
- Documentation: abstar.readthedocs.org
- Download: pypi.python.org/pypi/abstar
- Docker: hub.docker.com/r/brineylab/datascience/
install
bash
pip install abstar
use
To run abstar on a single FASTA or FASTQ file, you need to supply the input file and the project directory (into which output and logs will be written):
bash
abstar path/to/sequences.fasta path/to/project_directory
To iteratively run abstar on all files in an input directory, pass a directory containing FASTA or FASTQ files instead of the path to a single file:
bash
abstar path/to/input_directory path/to/project_directory
additional options
abstar contains a number of additional options and tools, including merging paired-end reads, parsing unique molecular identifiers (UMIs), and building/using custom germline databases. These are described in the abstar documentation.
api
Most core abstar functions are available through a Python API, making it easier to run abstar as a component of integrated analysis pipelines or to run abstar interactively (e.g. in a Jupyter notebook). See the abstar documentation for more detail about the API.
testing
You can run the complete abstar test suite by first installing pytest:
bash
pip install pytest
followed by:
bash
git clone https://github.com/brineylab/abstar
cd abstar
pytest
This test suite is automatically run after every commit, and is tested against all supported versions of Python.
requirements
Python 3.10+
abutils
click
matplotlib
numpy
pandas
parasail
polars
pyarrow
pytest
Owner
- Name: brineylab
- Login: brineylab
- Kind: organization
- Repositories: 1
- Profile: https://github.com/brineylab
GitHub Events
Total
- Create event: 9
- Release event: 4
- Issues event: 1
- Watch event: 2
- Delete event: 1
- Push event: 124
- Pull request event: 10
Last Year
- Create event: 9
- Release event: 4
- Issues event: 1
- Watch event: 2
- Delete event: 1
- Push event: 124
- Pull request event: 10
Committers
Last synced: almost 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Bryan Briney | b****y@g****m | 251 |
| bryanbriney | b****y@B****l | 214 |
| bryanbriney | b****y@d****u | 69 |
| S R Gokul Krishnan | s****r@g****m | 12 |
| bryanbriney | b****y@w****u | 11 |
| bryanbriney | b****y@w****u | 9 |
| bryanbriney | b****y@w****u | 6 |
| bryanbriney | b****y@w****u | 5 |
| Jordan Willis | j****0@g****m | 3 |
| Jordan Willis | j****s@s****u | 2 |
| Neil Dalchau | n****u@g****m | 2 |
| bryanbriney | b****y@w****u | 1 |
| bryanbriney | b****y@w****u | 1 |
| bryanbriney | b****y@w****u | 1 |
| CollinJ0 | 3****0 | 1 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
-
Total downloads:
- pypi 951 last-month
- Total dependent packages: 2
- Total dependent repositories: 3
- Total versions: 55
- Total maintainers: 1
pypi.org: abstar
Germline assignment and annotation of adaptive immune receptor repertoire (AIRR) data. Scalable from a single sequence to billions of sequences.
- Homepage: https://github.com/brineylab/abstar
- Documentation: https://abstar.readthedocs.io/
- License: MIT License
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Latest release: 0.7.3
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- sphinx >=1.3.1
- sphinx_rtd_theme *
- abutils >=0.2.9
- biopython ==1.78
- celery *
- dask *
- numpy >=1.16.5
- nwalign3 *
- pandas *
- pyarrow *
- pymongo *
- pytest *
- scikit-bio ==0.5.6