Fetch features from a list of accession or BioSample numbers.
Project description
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
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
- The simplest command. The output is in the current working directoy.
fetch_features -i path/to/list.txt -t accession -e email@address.com
- In this example, the output is in your Documents.
fetch_features -i path/to/list.txt -t accession -e email@address.com -o ~/Documents
- If you prefer the GUI version.
fetch_features --gui
Project details
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