Difference between revisions of "2018 Hakyung July Lab note"

Revision as of 01:36, 24 July 2018

== file = open ("/data2/haggui/RNA/edgeR/raw_edgeR/control.counts.edgeR","r") lines = file.readlines() list = [] for line in lines :

       gene_name = line.split('"')[1]  #"gene name" 으로 되어 있는 것 가져오기
       dic = [0,0,0,0,0]
       dic[0] = (gene_name) #dic = [genename,0,0,0,0]
       Cfile = open("/data2/haggui/RNA/edgeR/DEG_edgeR/DEG_control.txt","r") #control 상태에서의 DEG 정보
       Clines = Cfile.readlines()
       for Cline in Clines :
               Cgene_name = Cline.split('"')[1]
               ClogFC = float(Cline.split(' ')[1]) #logFC value
               if Cgene_name == gene_name :
                       if ClogFC < -1 :
                               dic[1] = dic[1]+1 # SS2-2 > TG 이면 1
                       elif ClogFC > 1 :
                               dic[1] = dic[1]+2 # TG < SS2-2 이면 2, dic = [genename,2,0,0,0]
                       else : pass
               else : pass
       Cfile.close()   
       Sfile = open("/data2/haggui/RNA/edgeR/DEG_edgeR/DEG_SS2-2.txt","r") #SS2-2가 drought 때 어떻게 변하는지
       Slines = Sfile.readlines()
       for Sline in Slines :
               Sgene_name = Sline.split('"')[1]
               SlogFC = float(Sline.split(' ')[1])
               if Sgene_name == gene_name :
                       if SlogFC > 1 :
                               dic[2] = dic[2]+1 # up-regulation이면 1
                       elif SlogFC < -1 : 
                               dic[2] = dic[2]+2 # down-regulation이면 2
                       else : pass
               else : pass
       Sfile.close()