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goaTools_MASTER.py
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executable file
·33 lines (22 loc) · 993 Bytes
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Jul 5 20:57:34 2020
@author: smith
"""
import ACWS_GOAtools as go
"""
Before starting anything in this script, open ACWS_GOAtools.py and change variables:
goaResultDir - change to path you want to save results to
genesDf - change to path to .xlsx file of differential expression data from scanPy
comparison - change to descriptor of data you are analyzing, example 'UpregulatedSaline'
"""
comparison = 'Clem_Oxy'
#Run for a single cluster
go._runGOanalysis('Cluster8', n_genes=75)
#Make a list of clusters and run for all. Change integer to number of clusters.
clusters = ['Cluster' + str(x) for x in range(16)]
newGeneIndex = go.runGOanalysis(clusters, processes=8)
#Combine individual cluster data files into one large data file
GOcategory = 'CC' #Can be 'MF' for molecular functions, 'BP' for biogical processes, or 'CC' for cellular components
go.combineGOresults(clusters, GOcategory, comparison)