Python package to automatically download datasets from GREIN
http://www.ilincs.org/apps/grein
To run our version of grein_loader, use the following code:
from pathlib import Path import sys
ROOT = Path.cwd().resolve().parent GREIN_LOADER_DIR = ROOT / "grein_loader" GREIN_LOADER_SRC = GREIN_LOADER_DIR / "src"
if str(GREIN_LOADER_SRC) not in sys.path: sys.path.insert(0, str(GREIN_LOADER_SRC))
print("workspace root:", ROOT) print("grein_loader dir:", GREIN_LOADER_DIR) print("grein_loader src:", GREIN_LOADER_SRC) print("using local src:", GREIN_LOADER_SRC.exists())
Grein Loader enables users to access data from the GREIN website by using the GSE identification number
Install the package from pypi by using:
pip install grein_loader
The package allows you to download the description, metadata and the raw counts of a GREIN dataset based on the GSE id. The datasets from GREIN are publicly available and can be accessed via the GREIN webpage. Each dataset uses an GEO accession id which allows you to access its data.
geo_accession = "GSE112749"
description, metadata, count_matrix = grein_loader.load_dataset(geo_accession)
Input/Output parameters
Input parameter:
| gse_id | string | GEO accession id
Output parameter:
| description | dictionary | description of dataset
| metadata | dictionary | metadata of dataset
| count_matrix | pandas dataframe| numpy array of raw counts
loads a number of datasets from Grein, the datasets are also listed on the main paige of GREIN
number_of_datasets = 10
overview = loader.load_overview(number_of_datasets)
The function returns a list of dictionaries, each dictionary contains the GSE id, number of samples, species and description provided from GREIN.
Input parameter:
number_of_samples
Output parameter:
list of dictionaries with, "geo_accession", no_samples", "species","title", "study_summary"