nsdpy 0.3.0b0

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

nsdpy

• Introduction
• Workfolw
• Quick start
• Usage
  • Google Colab
  • Command line
• Authors and acknowledgment
• Support
• Licence
• More Documentation

Introduction

nsdpy (nucleotide or NCBI sequence downloader) 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 nsdpy 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
• Select coding sequences from cds files based on the gene names using one or more regular expressions. This can help the user retrieve some sequences for which the gene name is annotated in another field.
• Retrieve the taxonomic information and add it to the output sequences.

Quick start

• Clone the repo from Github:

git clone https://github.com/RaphaelHebert/nsdpy.git

• pip:
  depending on the user environment pip may be replaced by pip3 if pip3 is used

pip install nsdpy

minimum python version for nsdpy: 3.8.2

• Google Colab: save a copy of this notebook in your drive.

Workflow

Usage

Google colab

nsdpy colab notebook

Command line

nsdpy -r "USER'S REQUEST" [OPTIONS] 

Authors and acknowledgment

Raphael Hebert
Emese Meglecz

Support

License

Code and documentation copyright 2021 the nsdpy authors. Code released under the MIT License.

More Documentation

Official documentation:
Readthedocs