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- Introduction
- Workflow
- Quick start
- Usage
- Authors and acknowledgment
- Support
- Licence
- More Documentation
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.
- 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 nsdpyminimum python version for nsdpy: 3.8.2
- Google Colab: save a copy of this notebook in your drive.
nsdpy -r "USER'S REQUEST" [OPTIONS]Code and documentation copyright 2021 the nsdpy authors. Code released under the MIT License.
Official documentation: Readthedocs