GEOdb 0.2.0.1

An asynchronous Python library for the Gene Expression Omnibus (GEO) database

GEOdb

An asynchronous Python library for the Gene Expression Omnibus (GEO) database

Usage

parser

from GEOdb.parser.series import parse_file, parse_item

Either parse a file:

parse_file('/path/to/GEO/downloaded.txt')

Or parse a text:

t = """1. Transcriptional profiling of human KIR+ CD8 T cells
(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:	Homo sapiens
Type:		Expression profiling by high throughput sequencing; Other
Platforms: GPL20301 GPL18573 4548 Samples
FTP download: GEO (TXT) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE193nnn/GSE193442/
Series		Accession: GSE193442	ID: 200193442"""

parse_item(t)

GEOSeriesInfo(title='Transcriptional profiling of human KIR+ CD8 T cells',
              link='https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193442',
              url='https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193442',
              summary='(Submitter supplied) This SuperSeries is composed of '
                      'the SubSeries listed below.',
              organism='Homo sapiens',
              type='Expression profiling by high throughput sequencing; Other',
              platform='GPL20301',
              samples=4548,
              id='GSE193442',
              accession='GSE193442',
              series_id=200193442,
              ftp='ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE193nnn/GSE193442/',
              sra=None)