nsdpy 0.1.12

Automatize the donwload of DNA sequences from NCBI, sort them according to their taxonomy and filter them with a gene name (provided as a regular expression)

NucleoPy

• Introduction
• workfolw
• Installation
• Usage
  • Google Colab
  • Command line
• Authors and acknowledgment
• Support
• Licence
• More Documentation

Introduction

NucleoPy aims to ease the download and sort of big bacth of DNA sequences from the NCBI database. It can also be usefull to filter the sequences based on their annotations. Using NucleoPy the user can:

• Search NCBI nucleotide database
• Download the fasta files or the cds_fasta files corresponding to the result of the search
• Sort the sequences based on their taxonomy
• Filter the sequences based on the name of the gene by giving one or more regular expression as filter(s)

Workflow

Installation

The package will be available from PyPI soon.

exepected:

pip3 install nucleopy

Usage

On google colab:

Nucleopy colab notebook

Command line

      python3 main.py -r USER'S REQUEST [OPTIONS] 

Authors and acknowledgment

Support

License

to choose, probably: https://choosealicense.com/licenses/gpl-3.0/

More Documentation

For examples of usage and more detailed documentation check: [Users manual on google doc](https://docs.google.com/document/d/1CJQg2Cv3P0lgWZRYd9xJQfj8qwIY4a-wtXa4VERdH2c/edit?usp=sharing =100)