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Copy pathsyuukei_counthap_1218.py
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syuukei_counthap_1218.py
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# arg: counthap
import sys
hikisuu = sys.argv
con_blo = {}
ookisa = {}
contigs_10X=[]
if len(hikisuu)-1 ==0:
sys.stderr.write("Error: no argument")
else:
for i in range(len(hikisuu)-1):
#filename=hikisuu[i+1].split("/")[-1]
filename=hikisuu[i+1].split("__")[-1]
filename=filename.split(".")[0]+filename.split(".")[1]
if not (filename in contigs_10X ):
contigs_10X.append(filename)
f1=open(hikisuu[i+1])
for lineline in f1:
if lineline != '\n':
linea=lineline.split()
if linea[0]=="rname":
pass
else:
if linea[2] == linea[3]:
pass
elif int(linea[2]) > int(linea[3]):
if linea[1] in con_blo:
con_blo[linea[1]][filename+"left"]=linea[2]+":"+linea[3]#+"@"+linea[2]+">"+linea[3])
else:
#con_blo[linea[1]]=[filename+"_left"+" :"+linea[2]+">"+linea[3]]
con_blo[linea[1]]={}
con_blo[linea[1]][filename+"left"]=linea[2]+":"+linea[3]#+"@"+linea[2]+">"+linea[3])
elif int(linea[3]) > int(linea[2]):
if linea[1] in con_blo:
con_blo[linea[1]][filename+"right"]=linea[2]+":"+linea[3]#+"@"+linea[2]+">"+linea[3])
else:
#con_blo[linea[1]]=[filename+"_right"+" :"+linea[3]+">"+linea[2]]
con_blo[linea[1]]={}
con_blo[linea[1]][filename+"right"]=linea[2]+":"+linea[3]#+"@"+linea[2]+">"+linea[3])
else:
sys.stderr.write("There may be strange row")
keyd = list(con_blo.keys())
valued=[]
for j in keyd:
valued.append([])
for l in con_blo[j].keys():
valued[-1].append(l)
#
# valued2 = con_blo.values()
# print(valued2)
# valued=[]
# for i in range(len(valued2)):
# valued.append(valued2[i].keys())
dotn={}
KOUNT=0
for i in contigs_10X:
KOUNT+=1
for k in range(len(con_blo)):
for l in range(len(valued[k])):
for m in range(l+1, len(valued[k])):
if keyd[k] in dotn:
dotn[keyd[k]].append({valued[k][l],valued[k][m]})
else:
dotn[keyd[k]]=[]
dotn[keyd[k]].append({valued[k][l],valued[k][m]})
valval=[]
for a in range(len(dotn.values())):
for b in list(dotn.values())[a]:
if b not in valval:
valval.append(b)
namae=contigs_10X[0].split("X")[0]+"X"
with open(namae+"counthap", "w") as f:
for k in valval:
st="#qname"
for ij in list(k):
st=st+" "+ij
f.write(st)
f.write('\n')
f.write('\n')
for iii in dotn:
for h in range(len(dotn[iii])):
#print(k, dotn[iii][h], "asd")
if dotn[iii][h]== k:
f.write(iii+" "+con_blo[iii][list(k)[0]]+" "+con_blo[iii][list(k)[1]])
f.write('\n')
f.write('\n')
f.write("#end")
f.write('\n')
#x10apb[dotn[i][j]]=i
contigs_10X_num=[]
contigs_10X_0=[]
for i in range(len(contigs_10X)):
num=contigs_10X[i].split("X")[1]
num0=contigs_10X[i].split("X")[0]
contigs_10X_num.append(num)
contigs_10X_0.append(num0+"X")
contigs_10X_num.sort()
contigs_10X_n1=[]
for i in range(len(contigs_10X)):
contigs_10X_n1.append(contigs_10X_0[0]+contigs_10X_num[i])
#print(contigs_10X_n)
cand1=[]
group1=[]
group2=[]
with open(namae+"counthap") as f:
for lineline in f:
if lineline != '\n':
linea=lineline.split()
if linea[0]=="#qname":
cand1.append([linea[1], linea[2]])
hikizan1=0
hikizan2=0
elif linea[0]=="#end":
cand1[-1].append(hikizan1)
cand1[-1].append(hikizan2)
else:
hikizan1=abs(int(linea[1].split(":")[0])-int(linea[1].split(":")[1]))+hikizan1
hikizan2=abs(int(linea[2].split(":")[0])-int(linea[2].split(":")[1]))+hikizan2
#contigs_10X_n.remove("B022_10X3967267")
#contigs_10X_n.remove("B022_10X5312547")
#contigs_10X_n.remove("B022_10X3977638")
#contigs_10X_n.remove("B022_10X5328797")
#contigs_10X_n.remove("B022_10X3978306")
#contigs_10X_n.remove("B022_10X3977582")
#
def group5(contigs_10X_n,cand):
#print(cand,"cand")
group1=[]
group2=[]
group1.append(contigs_10X_n[0]+"left")
group2.append(contigs_10X_n[0]+"right")
joutai=[]
for i in range(len(contigs_10X_n)-1):
kouho1=[0,0,0]
kouho2=[0,0,0]
kouho3=[0,0,0]
kouho4=[0,0,0]
for j in range(len(cand)):
if contigs_10X_n[i]+"left" in cand[j]:
if contigs_10X_n[i+1]+"left" in cand[j]:
kouho1=[contigs_10X_n[i+1]+"left",cand[j][2], cand[j][3]]
# if contigs_10X_n[i]+"left" in group1:
# group1.append(contigs_10X_n[i+1]+"left")
# if contigs_10X_n[i]+"left" in group2:
# group2.append(contigs_10X_n[i+1]+"left")
if contigs_10X_n[i+1]+"right" in cand[j]:
kouho2=[contigs_10X_n[i+1]+"right",cand[j][2], cand[j][3]]
# if contigs_10X_n[i]+"left" in group1:
# group1.append(contigs_10X_n[i+1]+"right")
# if contigs_10X_n[i]+"left" in group2:
# group2.append(contigs_10X_n[i+1]+"right")
if contigs_10X_n[i]+"right" in cand[j]:
if contigs_10X_n[i+1]+"left" in cand[j]:
kouho3=[contigs_10X_n[i+1]+"left", cand[j][2], cand[j][3]]
# if contigs_10X_n[i]+"right" in group1:
# group1.append(contigs_10X_n[i+1]+"left")
# if contigs_10X_n[i]+"right" in group2:
# group2.append(contigs_10X_n[i+1]+"left")
if contigs_10X_n[i+1]+"right" in cand[j]:
kouho4=[contigs_10X_n[i+1]+"right",cand[j][2], cand[j][3]]
# if contigs_10X_n[i]+"right" in group1:
# group1.append(contigs_10X_n[i+1]+"right")
# if contigs_10X_n[i]+"right" in group2:
# group2.append(contigs_10X_n[i+1]+"right")
# if (kouho1 != [0,0,0] and kouho2 != [0,0,0] and kouho3 !=[0,0,0] and kouho4 != [0,0,0]) or (kouho1 != [0,0,0] and kouho2 != [0,0,0] and kouho3 ==[0,0,0] and kouho4 != [0,0,0]) or (kouho1 != [0,0,0] and kouho2 == [0,0,0] and kouho3 != [0,0,0] and kouho4 != [0,0,0]) or(kouho1 != [0,0,0] and kouho2 != [0,0,0] and kouho3 !=[0,0,0] and kouho4 == [0,0,0]) or (kouho1 == [0,0,0] and kouho2 != [0,0,0] and kouho3 !=[0,0,0] and kouho4 != [0,0,0]):
cis=int(kouho1[1])*int(kouho1[2])+int(kouho4[1])*int(kouho4[2])
trans=int(kouho2[1])*int(kouho2[2])+int(kouho3[1])*int(kouho3[2])
if cis > trans:
if contigs_10X_n[i]+"right" in group1:
group1.append(contigs_10X_n[i+1]+"right")
if contigs_10X_n[i]+"right" in group2:
group2.append(contigs_10X_n[i+1]+"right")
if contigs_10X_n[i]+"left" in group1:
group1.append(contigs_10X_n[i+1]+"left")
if contigs_10X_n[i]+"left" in group2:
group2.append(contigs_10X_n[i+1]+"left")
else:
if contigs_10X_n[i]+"right" in group1:
group1.append(contigs_10X_n[i+1]+"left")
if contigs_10X_n[i]+"right" in group2:
group2.append(contigs_10X_n[i+1]+"left")
if contigs_10X_n[i]+"left" in group1:
group1.append(contigs_10X_n[i+1]+"right")
if contigs_10X_n[i]+"left" in group2:
group2.append(contigs_10X_n[i+1]+"right")
# if kouho1 != [0,0,0] and kouho2 == [0,0,0] and kouho3 ==[0,0,0] and kouho4 != [0,0,0]:
# joutai.append("Completetrans")
# elif kouho1 == [0,0,0] and kouho2 == [0,0,0] and kouho3 ==[0,0,0] and kouho4 == [0,0,0]:
# joutai.append("Completecis")
joutai.append([contigs_10X_n[i]])
for ki in range(len([kouho1, kouho2 , kouho3, kouho4])):
if [kouho1, kouho2 , kouho3, kouho4][ki] !=[0,0,0]:
if ki ==0:
joutai[-1].append("R-R")
if ki ==1:
joutai[-1].append("R-L")
if ki ==2:
joutai[-1].append("L-R")
if ki ==3:
joutai[-1].append("L-L")
joutai[-1].append(cis)
joutai[-1].append(trans)
joutai.append([contigs_10X_n[len(contigs_10X_n)-1]])
return group1, group2 , joutai
# if kouho1 != [0,0,0] and kouho2 == [0,0,0] and kouho3 ==[0,0,0] and kouho4 != [0,0,0]:
# joutai.append("Complete")
# if kouho1 != [0,0,0] and kouho2 == [0,0,0] and kouho3 ==[0,0,0] and kouho4 != [0,0,0]:
# joutai.append("Complete")
# if kouho1 != [0,0,0] and kouho2 == [0,0,0] and kouho3 ==[0,0,0] and kouho4 != [0,0,0]:
# if contigs_10X_n[i]+"right" in group1:
# group1.append(contigs_10X_n[i+1]+"right")
# if contigs_10X_n[i]+"right" in group2:
# group2.append(contigs_10X_n[i+1]+"right")
# if contigs_10X_n[i]+"left" in group1:
# group1.append(contigs_10X_n[i+1]+"left")
# if contigs_10X_n[i]+"left" in group2:
# group2.append(contigs_10X_n[i+1]+"left")
# if kouho1 == [0,0,0] and kouho2 != [0,0,0] and kouho3 !=[0,0,0] and kouho4 == [0,0,0]:
# if contigs_10X_n[i]+"right" in group1:
# group1.append(contigs_10X_n[i+1]+"left")
# if contigs_10X_n[i]+"right" in group2:
# group2.append(contigs_10X_n[i+1]+"left")
# if contigs_10X_n[i]+"left" in group1:
# group1.append(contigs_10X_n[i+1]+"right")
# if contigs_10X_n[i]+"left" in group2:
# group2.append(contigs_10X_n[i+1]+"right")
#
contigs_10X_n2=[]
contigs_10X_n3=[]
contigs_10X_n4=[]
contigs_10X_n5=[]
contigs_10X_n6=[]
for i in range(len(contigs_10X_n1)):
if i%2 == 0:
contigs_10X_n2.append(contigs_10X_n1[i])
else:
contigs_10X_n3.append(contigs_10X_n1[i])
for i in range(len(contigs_10X_n1)):
if i%3 == 0:
contigs_10X_n4.append(contigs_10X_n1[i])
elif i%3 == 1:
contigs_10X_n5.append(contigs_10X_n1[i])
elif i%3 == 2:
contigs_10X_n6.append(contigs_10X_n1[i])
sa1=group5(contigs_10X_n1,cand1)
sa2=group5(contigs_10X_n2,cand1)
sa3=group5(contigs_10X_n3,cand1)
sa4=group5(contigs_10X_n4,cand1)
sa5=group5(contigs_10X_n5,cand1)
sa6=group5(contigs_10X_n6,cand1)
for sa in [sa1,sa2,sa3,sa4,sa5,sa6]:
for i in sa:
print(i)
print("")
#dotf.write("}")
#
#lrg=[[],[]]
#
#for i in con_blo:
# if len(con_blo[i])>1:
# for j in range( len(con_blo[i])):
# if con_blo[i][j] in lrg[0]:
# #con_blo[i].pop(j)
# for k in range( len(con_blo[i])):
# lrg[0].append(con_blo[i][k])
# elif con_blo[i][j] in lrg[1]:
# #con_blo[i].pop(j)
# for k in range( len(con_blo[i])):
# lrg[1].append(con_blo[i][k])
#
#
#print(lrg)
#
#for i in con_blo:
# if len(con_blo[i])>1:
# for j in range( len(con_blo[i])):
# popd=[con_blo[i][j]]
# for k in con_blo:
# for l in range( len(con_blo[k])):
# if con_blo[k][l] ==popd:
# con_blo[i]=list(set(con_blo[i]+con_blo[k]))
#
#
#
#
#
#for i in con_blo:
# if len(con_blo[i])>1:
# print (con_blo[i])
#
# keyd2 = list(counthap2.keys())
# valued2 = list(counthap2.values())
# dotf.write("graph {")
# KOUNT = 0
# for i in range(len(counthap)):
# for j in range(len(valued[i])):
# searchob = valued[i][j].split("_")[0]
# searchob2 = valued[i][j].split("_")[1]
# for k in range(len(counthap)):
# for l in range(len(valued[k])):
# if searchob == valued[k][l].split("_")[0] and searchob2 != valued[k][l].split("_")[1]:
# dotf.write("subgraph cluster"+str(KOUNT)+" {"+'\n'+valued[i][j]+";"+'\n'+valued[k][l]+";"+'\n'+"}"+'\n')
# KOUNT+=1
#keyd = list(counthap.keys())
#valued = list(counthap.values())
#graph=[]
#for i in range(len(con_blo)):
# pbpb = keyd[i]
# graph.append([pbpb])
# for j in range(len(valued[i])):
# searchob = valued[i][j]
# for k in range(len(con_blo)):
# if k == i:
# pass
# else:
# for l in range(len(valued[k])):
# if searchob == valued[k][l]:
# graph[i].append(keyd[k])
#
#print(graph)