def __init__(self, config_filename):
GEOparse.set_verbosity("ERROR")
self.config_filename = config_filename
data_section = Utils.get_config(config_filename, 'GEOImporter')
self.config = GEOImporterConfig(**data_section)
self.logger = Utils.get_logger('GEOImporter')
self.storage = Storage(config_filename)
self.labels = self.config.labeling
self.inputs = self.config.input_data
self.control_labels = self.labels.control
self.type_labels = self.labels.type
self.gene_names = self.labels.gene_names
self.path = self.config.data_path
self.experiment_collumns = {}
Download the files to the paper
"Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region"
by Jeffrey R. Moffitt et al. 2018
http://science.sciencemag.org/content/362/6416/eaau5324
"""
from os import path
import GEOparse
if __name__ == '__main__':
debug = False
download_sra = False
gse_id = "GSE113576"
raw_dir = path.join(path.dirname(__file__), './raw')
if debug:
GEOparse.set_verbosity("DEBUG")
gse = GEOparse.get_GEO(geo=gse_id, destdir=raw_dir)
for n, meta in gse.metadata.items():
if 'supplementary_file' in n:
for url in meta:
dest = path.join(raw_dir, url.split('/')[-1])
if not path.exists(dest):
GEOparse.utils.download_from_url(url, dest, force=False)
for gsm, samp1 in gse.gsms.items():
break
if download_sra:
samp1.download_SRA('*****@*****.**', directory=raw_dir)
