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GSE Finder

is a geofetch class that provides functions to find and retrieve a list of GSE (GEO accession number) by using NCBI searching tool.

The main features of the geofetch Finder are:

  • Find GEO accession numbers (GSE) of the project that were uploaded or updated in certain period of time.
  • Use the same filter query as GEO DataSets Advanced Search Builder is using
  • Save list of the GSEs to file (This file with geo can be used later in geofetch)
  • Easier and faster to get GSEs using NCBI filter and certain period of time.

Tutorial

0) Initiale Finder object. 

from geofetch import Finder
gse_obj = Finder()

# Optionally: provide filter string and max number of retrieve elements
gse_obj = Finder(filters="((bed) OR narrow peak) AND Homo sapiens[Organism]", retmax=10)

1) Get list of all GSE in GEO 

gse_list =  gse_obj.get_gse_all()

2) Get list of GSE that were uploaded and updated last week 

gse_list = gse_obj.get_gse_last_week()

3) Get list of GSE that were uploaded and updated last 3 month 

gse_list = gse_obj.get_gse_last_3_month()

4) Get list of GSE that were uploaded and updated in las number of days 

# project that were uploaded in last 5 days:
gse_list = gse_obj.get_gse_by_day_count(5)

5) Get list of GSE that were uploaded in certain period of time 

gse_list = gse_obj.get_gse_by_date(start_date="2015/05/05", end_date="2020/05/05")

6) Save last searched list of items to the file 

gse_obj.generate_file("path/to/the/file")

# if you want to save different list of files you can provide it to the function
gse_obj.generate_file("path/to/the/file", gse_list=["123", "124"])

7) Compare two lists: 

new_gse_list = gse_obj.find_differences(list1, list2)

More information about gse and queries and id: - https://www.ncbi.nlm.nih.gov/geo/info/geo_paccess.html - https://newarkcaptain.com/how-to-retrieve-ncbi-geo-information-using-apis-part1/ - https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Using_the_Advanced_Search_Pag