Difference between revisions of "2018 Hakyung July Lab note"
From Crop Genomics Lab.
(→HT-seq, edgeR 처리 후 한 파일에 리스트 형태로 저장) |
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| − | =HT-seq, edgeR 처리 후 한 파일에 리스트 형태로 저장= | + | ==HT-seq, edgeR 처리 후 한 파일에 리스트 형태로 저장== |
file = open ("/data2/haggui/RNA/edgeR/raw_edgeR/control.counts.edgeR","r") | file = open ("/data2/haggui/RNA/edgeR/raw_edgeR/control.counts.edgeR","r") | ||
| Line 8: | Line 8: | ||
dic = [0,0,0,0,0] | dic = [0,0,0,0,0] | ||
dic[0] = (gene_name) #dic = [genename,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") | + | Cfile = open("/data2/haggui/RNA/edgeR/DEG_edgeR/DEG_control.txt","r") '''#control 상태에서의 DEG 정보''' |
Clines = Cfile.readlines() | Clines = Cfile.readlines() | ||
for Cline in Clines : | for Cline in Clines : | ||
Revision as of 01:42, 24 July 2018
HT-seq, edgeR 처리 후 한 파일에 리스트 형태로 저장
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()
Tfile = open("/data2/haggui/RNA/edgeR/DEG_edgeR/DEG_TG.txt","r")
Tlines = Tfile.readlines()
for Tline in Tlines :
Tgene_name = Tline.split('"')[1]
TlogFC = float(Tline.split(' ')[1])
if Tgene_name == gene_name :
if TlogFC > 1 :
dic[3] = dic[3]+1
elif TlogFC < -1 :
dic[3] = dic[3]+2
else : pass
else : pass
Tfile.close()
Dfile = open("/data2/haggui/RNA/edgeR/DEG_edgeR/DEG_drought.txt","r")
Dlines = Dfile.readlines()
for Dline in Dlines :
Dgene_name = Dline.split('"')[1]
DlogFC = float(Dline.split(' ')[1])
if Dgene_name == gene_name :
if DlogFC < -1 :
dic[4] = dic[4]+1
elif DlogFC > 1:
dic[4] = dic[4]+2
else : pass
else : pass
Dfile.close()
list.append(dic)
f = open('exp_list.txt','w') import pickle pickle.dump(list,f) f.close()
