automate_g2g1test.py

import sys

from resample_g2g1 import * #both scripts must be in the same directory; otherwise change path here


#this is the same as automate-g1_test scripts but uses the ranked file with g12 as the first column after gene and g2g1 as second

##Parameters##
essential_gene_path='/usr2/people/mabrams/Amended_Genomes/essential.csv' #change paths here to use elsewhere
gff='/usr2/people/mabrams/Amended_Genomes/S288C/saccharomyces_cerevisiae_R64-1-1_20110208_withoutFasta.gff'#and here
printLots=True #set to off for less output text 

#put the path for the g1 files to resample here
ranked_g12_paths={
    '1Wine':'/usr2/people/mabrams/data/g1_5top/1Wine/merged_1WineEuropean_ranked.txt',
    'M3': '/usr2/people/mabrams/data/g1_5top/M3/merged_M3_MosaicRegion3_ranked.txt',
    '8Mixed': '/usr2/people/mabrams/data/g1_5top/8Mixed/merged_8MixedOrigin_ranked.txt',
    '25Sake': '/usr2/people/mabrams/data/g1_5top/25Sake/merged_25Sake_ranked.txt',
    '3Brazil': '/usr2/people/mabrams/data/g1_5top/3Brazil/merged_3BrazilianBioethanol_ranked.txt'}


#and add the gene set(s) of interest for your analysis
goi_lists={

    'unpaired, reanalysis of Weiss et al. 2018 RH-Seq, mean, p_adj<0.05 - excluding YPR164W b/c no g1':[
        'YLR397C','YGR098C','YMR168C','YKR054C',
        'YHR023W','YDR180W','YPL174C','YCR042C',
        'YMR016C','YJR135C','YJL025W','YDR443C',
        'YKL134C'],
    }

##Functions##

def getResample(pop,goi_list,gff_genes):
    if printLots==True:
        print('\n\npopulation:\t'+pop)
    ranked_genes_G1=ranked_g12_paths[pop]
    tested_goi=test_goi_in_gff(goi_list,gff_genes,printGOI=printLots)
    essential_genes=ParseEssential(essential_gene_path)
    G12_dict=ParseRankedGenes(ranked_genes_G1,goi_list,printGeneG2G1=printLots)
    rv=resample(G12_dict,essential_genes,goi_list,printResampling=printLots) #resample that given G1 and don't print longform (gene by gene, num essential, etc)
    if (1-rv)*2<0.05:
        print(pop,str(rv)+'*')
        return rv, 's'
    else:
        print(pop, rv)
        return rv, 'ns'

def resampleAllCombos(ranked_g12_paths,goi_lists,gff_genes):
    for goi_list_desc in goi_lists:
        significant=0
        print('==='+goi_list_desc+'===')
        goi_list=goi_lists[goi_list_desc]
        for pop in ranked_g12_paths:
            p,sig=getResample(pop,goi_list,gff_genes)
            if sig=='s':
                significant+=1
        print('significant (1-rv)*2<0.05): ', significant)
            


###RUN###
if __name__ == "__main__":
    
    gff_genes=ParseFromGFF(gff)
    resampleAllCombos(ranked_g12_paths,goi_lists,gff_genes)