fetchm 0.1.7

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

Install in a New Conda Environment

conda create -n fetchm python=3.9
conda activate fetchm
pip install fetchM

Usage

Run FetchM with the following command:

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

For retrieving all available sequence data

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

For downloading sequences with sequence information

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

For downloading filtered sequences add the available Options below:

Options:

• --checkm CHECKM (Minimum CheckM completeness threshold, default: NA)
• --ani (Filter genomes by ANI status. Choices: OK, Inconclusive, Failed, all. Default is OK)
• --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 ncbi_dataset.tsv of your target organism(s) from the NCBI genome database. -ncbi_dataset.tsv

📋 Required Columns for ncbi_dataset.tsv in FetchM

Before running FetchM, ensure that your ncbi_dataset.tsv file includes the following columns. These columns are necessary for metadata enrichment, quality filtering, and downstream analysis.

---

🧬 Required Columns

Column Name	Description
Assembly Accession	Unique identifier for the assembly
Assembly Name	Name of the genome assembly
Organism Name	Scientific name of the organism
ANI Check status	Status of Average Nucleotide Identity (ANI) check
Annotation Name	Annotation version or label used
Assembly Stats Total Sequence Length	Total length (in base pairs) of all sequences in the assembly
Assembly BioProject Accession	Accession ID for the related BioProject
Assembly BioSample Accession	Accession ID for the related BioSample
Annotation Count Gene Total	Total number of genes annotated
Annotation Count Gene Protein-coding	Number of protein-coding genes
Annotation Count Gene Pseudogene	Number of pseudogenes
CheckM completeness	Completeness score from CheckM (in %)
CheckM contamination	Contamination score from CheckM (in %)

---

✅ Tips

• The file must be tab-separated (.tsv format).
• Don't change Column headers

---

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
  • Geographic Location_map.jpg
  • 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.