semvec/pypi-packages huggingface dataset:
danvers 1.0.0
Simple, file-based data version control

<img align="centre" alt="danvers" width="60" height="60" src="danvers.png" />

# danvers: simple file-based data version control

[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/joocer/danvers/blob/master/LICENSE)

**Danvers** is a Python data version management tool, which helps you to 
maintain and reference current and previous versions of data files. 

This means you can ensure code and models run consistently when they reference 
datasets that may change and that you can ensure you keep older copies of data
files used as part of decision making, so logic and code can be rerun.

New versions are only created if the new file is different to previous 
versions. This allows infrequently updated data sets to be easily maintained 
and versioned - if it's new, Danvers will keep a copy, if it hasn't changed,
it will ignore and keep its current version.

## Features
Danvers is simple, rather than feature-rich, but here are some of the things 
it can do:

- Access previous versions of data files
- Maintain a fixed number of verions (or all versions)
- Different trimming strategies are available (first-in-first-out, 
last-used-first-out) 
- Automatic duplicate check for data files against all known versions

## Dependencies
Danvers has no dependencies, just what comes with Python.

## Example Usage
~~~
from danvers import Danvers

# instantiate with the location the data is stored
vers = Danvers(r'data')

# create the dataset if it doesn't exist already
if not 'marvel_movies' in vers.read_datasets():
    vers.create_dataset('marvel_movies')

# add the first data file, should return verion 1
version = vers.create_data_file('marvel_movies', r'test_data\movies_phase_1.csv')
print(version)

# adding a new data file should return version 2
version = vers.create_data_file('marvel_movies', r'test_data\movies_phase_1+2.csv')
print(version)

# get the filename for the latest version of the data
filename = vers.get_data_file('marvel_movies')
print(filename)

# get the filename for version 1 of the data
filename = vers.get_data_file('marvel_movies', 1)
print(filename)
~~~

## License
[Apache 2.0](LICENSE)
rtd-phylogeny 0.0.51
Molecular phylogeny analysis using Return time distribution (RTD) based alignment-free sequence analysis method
Requires Python: >=3.7

![alt text](https://github.com/pandurang-kolekar/rtd-phylogeny/raw/master/data/RTD_Phylogeny.jpeg "RTD logo (c) Pandurang Kolekar 2017")

# RTD Phylogeny
Molecular phylogeny analysis using Return time distribution (RTD) based alignment-free sequence analysis method

### Author
Pandurang Kolekar, PhD Bioinformatics

![alt text](https://orcid.org/sites/default/files/images/orcid_16x16(1).gif "Logo ORCID") http://orcid.org/0000-0003-0044-0076

E-mail: pandurang.kolekar@gmail.com

Website: [http://biosakshat.wixsite.com/pandurang-kolekar](http://biosakshat.wixsite.com/pandurang-kolekar)
___

## Introduction

Return time distribution (RTD) is a method for alignment-free phylogenetic analysis using nucleotide / protein sequences. The method first computes the RTDs of k-mers and summarize them using the parameters of RTDs viz. mean and standard deviation for each of the sequences. Thus, each sequence is converted into a numeric vector of the size _2*4<sup>k</sup>_. The pair wise distance between numeric vectors of sequences is calculated using Euclidean distance function. The pairwise distance matrix, thus obtained is given as an input to Neighbor-joining clustering algorithm to reconstruct phyogenetic tree. 

The statistical details of the method are described in [Kolekar et al. 2012](https://www.ncbi.nlm.nih.gov/pubmed/22820020)

## Requirements

Tested on Python 3.7
Please refer to requirements.txt file

## Installation
```shell
pip install rtd-phylogeny
```
## Quick Start
```shell
python -m rtd_phylogeny --help
python -m rtd_phylogeny --version
python -m rtd_phylogeny --fastaFile <input_file> --seqType N --kmerSize 3
```

## Web Server

The web server for RTD-based phylogeny is available from [http://bioinfo.unipune.ac.in/RTD/](http://bioinfo.unipune.ac.in/RTD/).

## Perl Executables

The standalone Perl executables for RTD Phylogeny program are available from [http://bioinfo.unipune.ac.in/RTD/download.html](http://bioinfo.unipune.ac.in/RTD/download.html).

## Citation Information

If you find this program useful please cite it as following,

Kolekar P., Kale M., Kulkarni-Kale U., Alignment-free distance measure based on return time 
distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping, 
Molecular Phylogenetics and Evolution, (2012) 65(2): 510-522

PubMed ID: [22820020](https://www.ncbi.nlm.nih.gov/pubmed/22820020)

## Feedback

Please do feel free to give your comments / suggestions about this package by any of the following mode.

* Report an issue on this GitHub repository [here](https://github.com/pandurang-kolekar/rtd-phylogeny/issues)

* E-mail us at rtd.phylogeny@gmail.com

* Fill the feedback form for the RTD Phylogeny server: Available [here](https://docs.google.com/forms/d/e/1FAIpQLSel8RYKGQ3IIUxwjo0HgrDUyNv0ClNNwQETvguLUA2VYt0Odw/viewform)

Your feedback is highly valuable!