fetch features

Fetch information from a list of accession of BioSample numbers.

Installation

Create a virtual environment and install fetch features using pip as follows:

pip install fetch-features

You can also create a conda environment and install fetch features using pip.

Usage and options

To view all the options run:

fetch_features --help

Output:

usage: fetch_features [-h] [-v] [-i INPUT] [-t TYPE] [-e EMAIL] [-o OUTPUT] [-s SAVE_AS]
                      [--access-biosample-from-accession] [--gui]

Fetch features from a list of accession or BioSample numbers.

Help:
  -h, --help            Show this help message and exit.
  -v, --version         Show program's version number and exit

Required:
  -i INPUT, --input INPUT
                        Path to input file with list of unique identifiers (UIDs).
                        The user should provide the list of UIDs in a txt or xlsx file.
  -t TYPE, --type TYPE  Type of unique identifier: `accession` or `biosample`.
                        The `biosample` option fetches the information of the most
                        updated accession numbers associated with the BioSample number.
  -e EMAIL, --email EMAIL
                        Provide your email address to the NCBI.

Optional:
  -o OUTPUT, --output OUTPUT
                        Path to output folder (default current working directory).
  -s SAVE_AS, --save-as SAVE_AS
                        Save results as: `csv`, `excel`, or `csv-excel` (default `csv`).
  --access-biosample-from-accession
                        If you provide a list of accession numbers, get features of
                        all related accession numbers that belong to the same BioSample.
  --gui                 Activate GUI.

Usage examples

1. The simplest command. The output is in the current working directoy.

fetch_features -i path/to/list.txt -t accession -e email@address.com

2. In this example, the output is in your Documents.

fetch_features -i path/to/list.txt -t accession -e email@address.com -o ~/Documents

3. If you prefer the GUI version.

fetch_features --gui

Notes

Mac users can get the following error: "urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self-signed certificate in certificate chain (_ssl.c:1000)". To fix it run the following command in the terminal (chage the XX for the version of your Python) reference.

/Applications/Python\ 3.XX/Install\ Certificates.command