refseq-plasmid-dl 0.1.0

A command-line tool to download and curate RefSeq plasmid sequences from NCBI.

refseq-plasmid-dl

refseq-plasmid-dl is a Python command-line tool for downloading, parsing, filtering, and curating plasmid sequences from the NCBI RefSeq database. It provides flexible metadata filtering, sequence property filtering, and generates comprehensive reports and curated multi-FASTA files.

This project was heavily inspired by the excellent ncbi-genome-download tool, which is a staple for fetching bacterial assemblies. However, I found it difficult to specifically target and download only plasmid sequences using its existing filters. I built this tool to bridge that gap, providing a dedicated workflow for retrieving plasmid data from RefSeq without the overhead of filtering through full genome assemblies.

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Features

• Download Plasmid Sequences: Recursively fetches all gzipped FASTA files (.fna.gz) and GenBank files (.gbff.gz) from the NCBI RefSeq plasmid FTP/HTTPS directories.
• Metadata Extraction: Parses GenBank files to extract organism, taxonomy, plasmid name, strain, host, collection date, and other key metadata.
• Flexible Filtering: Filter sequences by:
  • Organism or Genus
  • NCBI Taxonomy ID
  • Strain, Isolate, Host, Plasmid Name, Geographic Location, Isolation Source
  • Sequence properties (minimum/maximum length, topology: circular/linear)
  • Record date or collection date
• Combining & Output: Generates a single curated multi-FASTA file and a CSV metadata table.
• Reporting: Produces a detailed summary report with counts of total records, filtered records by reason, and sequences written.
• Development Mode: Quick test download of a single file set for rapid testing.
• Reprocessing Existing Data: Skip download and re-run filtering/reporting on already downloaded files.

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Installation

Prerequisites

• Python 3.9+
• Internet access required for downloads and NCBI Entrez queries.

Using PyPI

pip install refseq-plasmid-dl

Using Bioconda

conda install -c bioconda refseq-plasmid-dl

From Source

git clone https://github.com/yourusername/refseq-plasmid-dl.git  
cd refseq-plasmid-dl  
pip install .

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Usage

The main command is:

refseq-plasmid-dl

Basic Download and Report

Download all RefSeq plasmids and generate metadata/report:

refseq-plasmid-dl

Curating Specific Organism or Topology

Download and retain circular plasmids for a specific organism, e.g., Salmonella:

refseq-plasmid-dl --outdir Salmonella_plasmids --organism Salmonella --topology circular

Reprocessing Existing Files

Skip download and apply new filters to an existing directory:

refseq-plasmid-dl --indir existing_data --organism Escherichia --topology circular

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Command-Line Arguments

Argument	Shorthand	Default	Description
--outdir	-o	refseq_plasmids	Output directory for FASTA files, reports, and metadata.
--indir	-i	None	Use existing download directory, skip FTP/HTTPS download.
--dev-mode	-d	False	Development mode: download a single test file set.
--force		False	Force re-download of existing files.
--organism	-s	all	Filter by species/organism (substring match).
--taxid	-t	all	Filter by NCBI Taxonomy ID.
--strain		None	Filter by strain.
--isolate		None	Filter by isolate.
--host		None	Filter by host organism.
--plasmid-name		None	Filter by plasmid name.
--geo_loc_name		None	Filter by geographic location.
--isolation_source		None	Filter by isolation source.
--min-length		None	Minimum sequence length (bp).
--max-length		None	Maximum sequence length (bp).
--topology		circular	Filter by topology: circular, linear, or all.
--min-date		None	Include only records updated after YYYY-MM-DD.
--max-date		None	Include only records updated before YYYY-MM-DD.
--min-collection-date		None	Include only records collected after YYYY-MM-DD.
--max-collection-date		None	Include only records collected before YYYY-MM-DD.
--version	-v		Show program version.

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Output Directory Structure

[OUTDIR]/  
├── plasmids_index.html                 # Saved HTML listing of NCBI plasmid directory  
├── refseq_plasmids/                    # Raw downloaded FASTA and GBFF files  
│   ├── plasmid.*.genomic.fna.gz  
│   └── plasmid.*.genomic.gbff.gz  
├── refseq_plasmids_dl.fasta            # Final curated multi-FASTA  
├── refseq_plasmids_dl_metadata.csv     # Full metadata for filtered plasmids
└── refseq_plasmids_dl_report.csv       # Summary report with filter  

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Examples

Download all plasmids and generate report

refseq-plasmid-dl --topology all

Filter by organism and circular topology

refseq-plasmid-dl --organism Escherichia --topology circular

Skip download and reprocess existing data

refseq-plasmid-dl --indir refseq_plasmids --min-length 5000 --max-length 200000

Note on AI Assistance

Parts of this codebase and documentation were drafted with the help of Google Gemini. The AI was used primarily for creating the project outline, writing development logic, and generating test cases. The final logic and implementation details have been verified manually.

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License

This project is licensed under the GNU General Public License v3.0 (GPL-3.0). See the LICENSE file for full details.