Difference between revisions of "2018 Hakyung July Lab note"
From Crop Genomics Lab.
(Created page with "== 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] #"...") |
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− | == | + | =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() | + | file = open ("/data2/haggui/RNA/edgeR/raw_edgeR/control.counts.edgeR","r") |
− | list = [] | + | lines = file.readlines() |
− | for line in lines : | + | list = [] |
+ | for line in lines : | ||
gene_name = line.split('"')[1] #"gene name" 으로 되어 있는 것 가져오기 | gene_name = line.split('"')[1] #"gene name" 으로 되어 있는 것 가져오기 | ||
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") {{색|blue|'''control 상태에서의 DEG 정보'''}} |
Clines = Cfile.readlines() | Clines = Cfile.readlines() | ||
for Cline in Clines : | for Cline in Clines : | ||
Line 33: | Line 34: | ||
else : pass | else : pass | ||
Sfile.close() | 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() |
Revision as of 01:40, 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") Template:색 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()