Gets metadata of GSM accession using GEOmetadb.sqlite

geo_metadata.ipynb

import sqlite3

# from https://gbnci-abcc.ncifcrf.gov/geo/
geo_db = "GEOmetadb.sqlite"

# connects to the database
sra_con = sqlite3.connect(geo_db)
cursor = sra_con.cursor()

gsms = ['GSM409307', 'GSM1220601', 'GSM1120314', 'GSM1120315', 'GSM1112815', 'GSM1112816', 'GSM1112817', 'GSM1112818', 'GSM410808']

#cursor.execute("PRAGMA table_info(gsm);")
for gsm in gsms:
    cursor.execute("SELECT source_name_ch1 FROM gsm WHERE gsm='%s';" % gsm)
    print cursor.fetchall()