# 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:
```bash
pip install fetch-features
```
## Usage and options
To view all the options run:
```bash
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.
```bash
fetch_features -i path/to/list.txt -t accession -e email@address.com
```
2. In this example, the output is in your Documents.
```bash
fetch_features -i path/to/list.txt -t accession -e email@address.com -o ~/Documents
```
3. If you prefer the GUI version.
```bash
fetch_features --gui
```
<p align='center'>
<img src=https://github.com/ivanmugu/fetch_features/blob/main/images/fetch_features_gui.png />
</p>
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"description": "# fetch features\n\nFetch information from a list of accession of BioSample numbers.\n\n## Installation\n\nCreate a virtual environment and install `fetch features` using pip as follows:\n\n```bash\npip install fetch-features\n```\n\n## Usage and options\n\nTo view all the options run:\n\n```bash\nfetch_features --help\n```\n\nOutput:\n\n```\nusage: fetch_features [-h] [-v] [-i INPUT] [-t TYPE] [-e EMAIL] [-o OUTPUT] [-s SAVE_AS]\n [--access-biosample-from-accession] [--gui]\n\n __ _ _ __ _\n / _| ___| |_ ___| |__ / _| ___ __ _| |_ _ _ _ __ ___ ___\n| |_ / _ \\ __/ __| '_ \\ | |_ / _ \\/ _` | __| | | | '__/ _ \\/ __|\n| _| __/ || (__| | | | | _| __/ (_| | |_| |_| | | | __/\\__ \\\n|_| \\___|\\__\\___|_| |_| |_| \\___|\\__,_|\\__|\\__,_|_| \\___||___/\n\nFetch features from a list of accession or BioSample numbers.\n\nHelp:\n -h, --help Show this help message and exit.\n -v, --version Show program's version number and exit\n\nRequired:\n -i INPUT, --input INPUT\n Path to input file with list of unique identifiers (UIDs).\n The user should provide the list of UIDs in a txt or xlsx file.\n -t TYPE, --type TYPE Type of unique identifier: `accession` or `biosample`.\n The `biosample` option fetches the information of the most\n updated accession numbers associated with the BioSample number.\n -e EMAIL, --email EMAIL\n Provide your email address to the NCBI.\n\nOptional:\n -o OUTPUT, --output OUTPUT\n Path to output folder (default current working directory).\n -s SAVE_AS, --save-as SAVE_AS\n Save results as: `csv`, `excel`, or `csv-excel` (default `csv`).\n --access-biosample-from-accession\n If you provide a list of accession numbers, get features of\n all related accession numbers that belong to the same BioSample.\n --gui Activate GUI.\n```\n\n## Usage examples\n\n1. The simplest command. The output is in the current working directoy.\n\n```bash\nfetch_features -i path/to/list.txt -t accession -e email@address.com\n```\n\n2. In this example, the output is in your Documents.\n\n```bash\nfetch_features -i path/to/list.txt -t accession -e email@address.com -o ~/Documents\n```\n\n3. If you prefer the GUI version.\n\n```bash\nfetch_features --gui\n```\n\n<p align='center'>\n <img src=https://github.com/ivanmugu/fetch_features/blob/main/images/fetch_features_gui.png />\n</p>\n",
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