semvec/pypi-packages huggingface dataset:
racpy 0.1.6
RNASeq Age Calculation in Python
License: MIT license
Requires Python: >=3.5
Keywords: racpy

=====
racpy
=====


.. image:: https://img.shields.io/pypi/v/racpy.svg
        :target: https://pypi.python.org/pypi/racpy

.. image:: https://img.shields.io/travis/reese3928/racpy.svg
        :target: https://travis-ci.com/reese3928/racpy

.. image:: https://readthedocs.org/projects/racpy/badge/?version=latest
        :target: https://racpy.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status


.. image:: https://pyup.io/repos/github/reese3928/racpy/shield.svg
     :target: https://pyup.io/repos/github/reese3928/racpy/
     :alt: Updates



RNASeq Age Calculation in Python


* Free software: MIT license
* Documentation: https://racpy.readthedocs.io.


Features
--------

This is the Python verion of our proposed multi-tissue transcriptional age calculator.

* The RNAAgeCalc paper can be found here https://doi.org/10.1371/journal.pone.0237006.
* The Python package can be found here https://pypi.org/project/racpy.
* The Python package documentation can be found here https://racpy.readthedocs.io.
* An interactive Shiny App can be found here https://xuren2120.shinyapps.io/RNAAgeCalcshiny/.    
* The Shiny App demo can be found here http://www.ams.sunysb.edu/~pfkuan/RNAAgeCalc/instructions.html.  
* The R version can be found here https://bioconductor.org/packages/release/bioc/html/RNAAgeCalc.html.   

Authors
--------

* `Xu Ren <https://github.com/reese3928>`__ <xuren2120@gmail.com>
* `Pei Fen Kuan <http://www.ams.sunysb.edu/~pfkuan/>`__ <peifen.kuan@stonybrook.edu>

Credits
-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

Dependencies scanned by PyUp.io

Citation
--------
Ren, X., & Kuan, P. F. (2020). RNAAgeCalc: A multi-tissue transcriptional age calculator. PloS one, 15(8), e0237006. 

| @article{ren2020rnaagecalc, 
| title={RNAAgeCalc: A multi-tissue transcriptional age calculator},    
| author={Ren, Xu and Kuan, Pei-Fen},    
| journal={PLOS ONE},    
| volume={15},    
| number={8},    
| pages={1-21},    
| year={2020},    
| publisher={Public Library of Science}    
| }

=======
History
=======
0.1.6 (2020-09-20)
------------------

* Added citation

0.1.5 (2020-06-24)
------------------

* Replaced "DESeq" with "DESeq2" throughout the package

0.1.4 (2020-06-10)
------------------

* Updated requirements_dev.txt

0.1.3 (2020-04-24)
------------------

* Included extra credits in README 

0.1.2 (2020-02-18)
------------------

* Bug fixes.

0.1.0 (2020-02-09)
------------------

* Package created. First release on PyPI.
devtools-shorthand-sql 0.4.0
Aid writing boilerplate SQL items from create tables, inserts and updates.
License: MIT license
Requires Python: >=3.6
Keywords: devtools_shorthand_sql

# devtools_shorthand_sql

[![image](https://img.shields.io/pypi/v/devtools_shorthand_sql.svg)](https://pypi.python.org/pypi/devtools_shorthand_sql/)
[![image](https://img.shields.io/pypi/l/devtools_shorthand_sql.svg)](https://pypi.python.org/pypi/devtools_shorthand_sql/)
[![image](https://img.shields.io/pypi/pyversions/devtools_shorthand_sql.svg)](https://pypi.python.org/pypi/devtools_shorthand_sql/)
[![Travis](https://img.shields.io/travis/HaeckelK/devtools_shorthand_sql/master.svg?logo=travis)](https://travis-ci.org/HaeckelK/devtools_shorthand_sql)
[![readthedocs](https://readthedocs.org/projects/devtools-shorthand-sql/badge/?version=latest)](https://devtools-shorthand-sql.readthedocs.io/en/latest/?badge=latest)
[![codecov](https://codecov.io/gh/HaeckelK/devtools_shorthand_sql/branch/master/graph/badge.svg)](https://codecov.io/gh/HaeckelK/devtools_shorthand_sql)

## Overview

Aid for writing boilerplate python code for SQL work, including creation of tables, insert functions, unit testing and SQL, dependent on relational database management system selected.

- Documentation: https://devtools-shorthand-sql.readthedocs.io.

## Quickstart

Install the latest version of this software from the Python package index (PyPI):
```bash
pip install --upgrade devtools_shorthand_sql
```

Create a shorthand sql file e.g. shorthand.txt.
```
# photo
id,id
size,int
filename,text
date_taken,int
```

Run
```bash
devtools_shorthand_sql shorthand.txt
```

Notification that file created:
```bash
Info: Output saved to: shorthand_sql_created_functions.txt
```

Created file contains:

SQL statement for table creation:
```SQL
CREATE TABLE IF NOT EXISTS photo (
id INTEGER PRIMARY KEY,
size INT,
filename TEXT,
date_taken INT
);
```

Python function for data insertion:
```python
def insert_photo(id: int, size: int, filename: str, date_taken: int) -> int:
    params = (id, size, filename, date_taken)
    id = YOUR_CONNECTOR_EXECUTOR("""INSERT INTO photo (id, size, filename, date_taken) VALUES(?,?,?,?);""",
                                 params)
    return id
```

Python function for unit testing (pytest only):
```python
def test_insert_photo(YOUR_CLEAN_DB_FIXTURE):
    expected = (1, 160, '3RWL0C6QSU', 374)
    new_id = YOUR_MODULE.insert_photo(size=160, filename="3RWL0C6QSU", date_taken=374)
    result = YOUR_CONNECTOR_QUERY('SELECT * FROM photo').fetchall()[0]
    assert result == expected
    assert new_id == 1
```

## Requirements

Python 3.6 or later is required to run devtools_shorthand_sql.

No other third party packages are required.