fetchm 0.1.3

A Python tool for fetching metadata for bacterial genomes.

FetchM: Metadata Fetching and Analysis Tool

Overview

FetchM is a Python-based tool for fetching and analyzing genomic metadata from NCBI BioSample records. When you download ncbi_dataset.tsv from the NCBI genome database, the metadata fields such as 'Collection Date', 'Host', 'Geographic Location', and 'Isolation Source' are missing. This tool helps fetch the associated metadata for each BioSample ID. FetchM requires an input file (ncbi_dataset.tsv) from the NCBI genome database, retrieves additional annotations from NCBI, filters the data based on quality thresholds, and generates visualizations to help interpret the results. You can also download the filtered sequences.

Features

• Fetch metadata from NCBI BioSample API.
• Filter genomes based on CheckM completeness and ANI check status.
• Generate metadata summaries and annotation statistics.
• Create various visualizations for geographic distribution, collection dates, gene counts, continent, and subcontinent.
• Download genome sequences (optional).
• Download sequences after filtering by host species, year, country, continent, and subcontinent.

Installation

Option 1: Install via Conda (Recommended)

conda install -c conda-forge fetchM

Option 2: Install in a New Conda Environment (Isolated)

conda create -n fetchM_env -c conda-forge fetchM
conda activate fetchM_env

Option 3: Install via pip

pip install fetchM

Usage

Run FetchM with the following command:

fetchM --input input.tsv --outdir results/

Additional Options:

• --checkm CHECKM (Minimum CheckM completeness threshold, default: 95)
• --sleep (Time to wait between requests, default: 0.5s)
• --seq (Enable sequence download mode)

Downloading sequences based on different criteria

• --host HOST [HOST ...] (Filter by host species, e.g., "Homo sapiens" "Bos taurus")
• --year YEAR [YEAR ...] (Filter by year or year range, e.g., "2015" "2018-2025")
• --country COUNTRY [COUNTRY ...] (Filter by country, e.g., "Bangladesh" "United States")
• --cont CONT [CONT ...] (Filter by continent, e.g., "Asia" "Africa")
• --subcont SUBCONT [SUBCONT ...] (Filter by subcontinent, e.g., "Southern Asia" "Western Africa")

Input

Download the ncbi_dataset.tsv from NCBI genome database for your target organism -ncbi_dataset.tsv

Output

FetchM creates a subdirectory in /results/ based on the organism name provided in the input file. Inside this subdirectory, the following folders are created:

• Metadata summaries in metadata_output/
  • annotation_summary.csv
  • assembly_summary.csv
  • metadata_summary.csv
  • ncbi_clean.csv
  • ncbi_filtered.csv
  • ncbi_dataset_updated.tsv
• Figures in figures/
  • Annotation Count Gene Protein-coding_distribution.tiff
  • Annotation Count Gene Pseudogene_distribution.tiff
  • Annotation Count Gene Total_distribution.tiff
  • Assembly Stats Total Sequence Length_distribution.tiff
  • Collection Date_bar_plots.tiff
  • Continent_bar_plots.tiff
  • Geographic Location_bar_plots.tiff
  • Host_bar_plots.tiff
  • scatter_plot_gene_protein_coding_vs_collection_date.tiff
  • scatter_plot_gene_total_vs_collection_date.tiff
  • scatter_plot_total_sequence_length_vs_collection_date.tiff
  • Subcontinent_bar_plots.tiff
• Sequences in sequences/ (if --seq is enabled, it will contain the downloaded genome sequences).

Visualizations

Annotation Distributions

Assembly Statistics

Metadata Summaries

Scatter Plots

License

This project is licensed under the MIT License.

Author

Developed by Tasnimul Arabi Anik.

Contributions

Contributions and improvements are welcome! Feel free to submit a pull request or report issues.