GEOparse

geoparse.py

# GEOparse download GEO series as SOFT files, and supplementary fiels to use locally
# load as easy to manipulate objects
# prepare dataset for GEO upload

import GEOparse

gse = GEOparse.get_GEO(geo="GSE1563", destdir="./")
# check GEO database for accession ID and download to CWD

# if already downloaded... use to read file into GSE object
# gse = GEOparse.get_GEO(filepath="./GSE1563.soft.gz")


print()
print("GSM example:")
for gsm_name, gsm in gse.gsms.items():
    print("Name: ", gsm_name)
    print("Metadata:",)
    for key, value in gsm.metadata.items():
        print(" - %s : %s" % (key, ", ".join(value)))
    print ("Table data:",)
    print (gsm.table.head())
    break

print()
print("GPL example:")
for gpl_name, gpl in gse.gpls.items():
    print("Name: ", gpl_name)
    print("Metadata:",)
    for key, value in gpl.metadata.items():
        print(" - %s : %s" % (key, ", ".join(value)))
    print("Table data:",)
    print(gpl.table.head())
    break