<!-- markdownlint-disable -->
<h2 align="center" style="font-family:verdana;font-size:150%"> <b>S</b>equencing <b>A</b>nalysis and <b>D</b>ata Library for <b>I</b>mmunoinformatics <b>E</b>xploration</h2>
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## About
---
<!-- use a href so you can use _blank to open new tab -->
**Documentation**: <a href="https://sadie.jordanrwillis.com" target="_blank">https://sadie.jordanrwillis.com</a>
**Source Code**: <a href="https://github.com/jwillis0720/sadie" target="_blank">https://github.com/jwillis0720/sadie</a>
**Colab**: [https://colab.research.google.com/github/jwillis0720/sadie](https://colab.research.google.com/github/jwillis0720/sadie/blob/main/notebooks/airr_c/SADIE_DEMO.ipynb)
---
SADIE is the **S**equencing **A**nalysis and **D**ata library for **I**mmunoinformatics **E**xploration. The key feautures include:
- Provide pre-built **command line applications** for popular immunoinformatics applications.
- Provide a **low-level API framework** for immunoinformatics developers to build higher level tools.
- Provide a **testable** and **reusable** library that WORKS!
- Provide a **customizable** and **verified** germline reference library.
- Maintain data formats consistent with standards governed by the [**AIRR community**](https://docs.airr-community.org/en/stable/#table-of-contents)
- **Portability** ready to use out the box.
SADIE is billed as a "**complete antibody library**", not because it aims to do everything, but because it aims to meet the needs of all immunoinformatics users. SADIE contains both low, mid and high level functionality for immunoinformatics tools and workflows. You can use SADIE as a framework to develop your own tools, use many of the prebuilt contributed tools, or run it in a notebook to enable data exploration. In addition, SADIE aims to port all code to python because relies heavily on the [Pandas](https://www.pandas.org) library, the workhorse of the data science/machine learning age.
## Installation
---
Installation is handled using the python package installer `pip`
```console
$ pip install sadie-antibody
```
### Development installation.
Pull requests are highly encouraged [here](https://github.com/jwillis0720/sadie/pulls). The development installation uses [pre-commit](https://pre-commit.com/), [flake8](https://flake8.pycqa.org/en/latest/) linting and [black](https://github.com/psf/black) style formatting to maintain code readability and reausability.
```console
$ git clone git@github.com/jwillis0720/sadie.git
$ pip install poetry
$ poetry install --with dev
```
## Quick Usage
Consult the [documentation](https://sadie.jordanrwillis.com) for complete usage. Or checkout our [Colab](https://colab.research.google.com/github/jwillis0720/sadie/blob/main/notebooks/airr_c/SADIE_DEMO.ipynb) notebook
### Command Line Usage
Annotate antibody sequences only from functional human imgt antibodies to a gzip output
```console
$ sadie airr my_sequence.fasta
```
### API
```python
from sadie.airr import Airr
# define a single sequence
pg9_seq = """
CAGCGATTAGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGTCGTCCCTGAGACTCTCCTGTGCAGCGT
CCGGATTCGACTTCAGTAGACAAGGCATGCACTGGGTCCGCCAGGCTCCAGGCCAGGGGCTGGAGTGGGT
GGCATTTATTAAATATGATGGAAGTGAGAAATATCATGCTGACTCCGTATGGGGCCGACTCAGCATCTCC
AGAGACAATTCCAAGGATACGCTTTATCTCCAAATGAATAGCCTGAGAGTCGAGGACACGGCTACATATT
TTTGTGTGAGAGAGGCTGGTGGGCCCGACTACCGTAATGGGTACAACTATTACGATTTCTATGATGGTTA
TTATAACTACCACTATATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCGAGC""".replace(
"\n", ""
)
# initialize the api
air_api = Airr("human")
# run single sequence string
airr_table = air_api.run_single("PG9", pg9_seq)
```
## License
[](https://opensource.org/licenses/MIT)
- Copyright © Jordan R. Willis, Troy M. Sincomb & Caleb K. Kibet
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The key feautures include:\n\n- Provide pre-built **command line applications** for popular immunoinformatics applications.\n\n- Provide a **low-level API framework** for immunoinformatics developers to build higher level tools.\n\n- Provide a **testable** and **reusable** library that WORKS!\n\n- Provide a **customizable** and **verified** germline reference library.\n\n- Maintain data formats consistent with standards governed by the [**AIRR community**](https://docs.airr-community.org/en/stable/#table-of-contents)\n\n- **Portability** ready to use out the box.\n\nSADIE is billed as a \"**complete antibody library**\", not because it aims to do everything, but because it aims to meet the needs of all immunoinformatics users. SADIE contains both low, mid and high level functionality for immunoinformatics tools and workflows. You can use SADIE as a framework to develop your own tools, use many of the prebuilt contributed tools, or run it in a notebook to enable data exploration. 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