def generateTErecurencematrixbaseonLISTdistanceForOneChr(repository,endofthefile,achr,windowsize):
dumpmatname=repository+achr+endofthefile+"dumpmat.dump"
if op.exists(dumpmatname):
print("===> Matrice deja existante")
thematrix=pickle.load(open(dumpmatname,"rb"))
else:
print("===>Constitution de la matrice")
filename=repository+achr+endofthefile
setlist,sizelist=generatedoublelistofset(filename,windowsize)
L=len(setlist)
Lset=windowsize #juste for speed writing
print(L)
thematrix=np.zeros((L,L))
i=0
j=0
print("====>Creation de la matrice")
print(thematrix.shape)
while i<L:
print(i)
while j<L:
if j>i:
val=distancebetweenlist(setlist[i],setlist[j])
thematrix[i,j]=val
thematrix[j,i]=val
j+=1
j=0
i+=1
print("====>Dumping de la matrice")
pickle.dump(thematrix,open(dumpmatname,"wb")) #other option of dump but with bigger file
print("===> Afichage de la matrice")
manipname=repository+achr+endofthefile+"recurenceplot.png"
print(thematrix.shape)
#print(np.where(thematrix<0))
utils.showamatwithcolorcode(np.add(thematrix,1),manipname,"hot_r") #jet<bwr
return thematrix
def generateTErecurencematrixHicComparableForOneChr(repository,endofthefile,achr,resolution,chrsizepath,species):
dumpmatname=repository+achr+endofthefile+"dumpmatHiCbin.dump"
densityname=repository+achr+endofthefile
if op.exists(dumpmatname+".npy"):
print("===> Matrice deja existante")
thematrix=np.load(open(dumpmatname+".npy","rb"))
else:
print("===>Constitution de la matrice")
filename=repository+achr+endofthefile
print("resolution:",resolution)
sizedict=utils.loadchrsizedict(chrsizepath,resolution)
#find the size of the list of list base on distance
sizeList=findsizeforHicListofList(sizedict,utils.dictchr[species],achr)
print("taille de la liste:",sizeList)
setlist=generateHicListofpattern(filename,sizeList,resolution)
transformHiClistofpatterninDensity(setlist,"LTR/Gypsy",densityname+"Gypsy")
transformHiClistofpatterninDensity(setlist,"LINE/CR1",densityname+"CR1")
transformHiClistofpatterninDensity(setlist,"DNA/P",densityname+"DNAP")
transformHiClistofpatterninDensity(setlist,"RC/Helitron",densityname+"helitron")
print("taille de la setlist",len(setlist))
L=sizeList #in theory len(setlist)==sizeList
#Lset=windowsize #juste for speed writing
print("==>Taille de la matrice:",L)
thematrix=np.zeros((L,L))
i=0
j=0
while i<L:
print(i)
while j<L:
if j>=i:
val=distancebetweenunequallist3(setlist[i],setlist[j])
thematrix[i,j]=val
thematrix[j,i]=val
j+=1
j=0
i+=1
print("====>Dumping de la matrice")
#pickle.dump(thematrix,open(dumpmatname,"wb")) #other option of dump but with bigger file
#toto={}#just to be un matlab savemat format
#toto['mat']=thematrix
#scpio.savemat(repository+achr+endofthefile+"TErecurencematrix.mat",toto)
np.save(dumpmatname, thematrix)
"""cormat=np.corrcoef(thematrix)
v,e=giveeigenvalueandvectorvalue(cormat,10)
utils.savematrixasfilelist3(e[:,0],repository+achr+"Corrv1")
utils.savematrixasfilelist3(e[:,1],repository+achr+"Corrv2")
utils.savematrixasfilelist3(e[:,2],repository+achr+"Corrv3")
utils.savematrixasfilelist3(e[:,3],repository+achr+"Corrv4")"""
print("===> Afichage de la matrice")
manipname=repository+achr+endofthefile+"recurenceplot.png"
print(thematrix.shape)
#print(np.where(thematrix<0))
utils.showamatwithcolorcode(thematrix,manipname,"bwr") #jet<bwr
return thematrix
def fastop(repository,endofthefile,achr,resolution,chrsizepath,species):
dumpmatname=repository+achr+endofthefile+"dumpmatHiCbin.dump"
thematrix=np.load(open(dumpmatname+".npy","rb"))
cormat=np.corrcoef(thematrix)
where_are_NaNs =np.isnan(cormat)
cormat[where_are_NaNs] = 0
where_are_NaNs =np.isinf(cormat)
cormat[where_are_NaNs] = 0
"""v,e=giveeigenvalueandvectorvalue(cormat,10)
utils.savematrixasfilelist3(e[:,0],repository+achr+"Corrv1")
utils.savematrixasfilelist3(e[:,1],repository+achr+"Corrv2")
utils.savematrixasfilelist3(e[:,2],repository+achr+"Corrv3")
utils.savematrixasfilelist3(e[:,3],repository+achr+"Corrv4")"""
print("===> Afichage de la matrice")
manipname=repository+achr+endofthefile+"Corrrecurenceplot.png"
print(thematrix.shape)
#print(np.where(thematrix<0))
utils.showamatwithcolorcode(cormat,manipname,"bwr") #jet<bwr
def generateTErecurencematrixbaseonSETdistanceForOneChr(repository,endofthefile,achr,windowsize):
dumpmatname=repository+achr+endofthefile+"dumpmat.dump"
if op.exists(dumpmatname):
print("===> Matrice deja existante")
#thematrix=scpio.loadmat(dumpmatname)['mat']
thematrix=pickle.load(open(dumpmatname,"rb"))
else:
print("===>Constitution de la matrice")
filename=repository+achr+endofthefile
setlist,sizelist=generatejumplistofset(filename,windowsize)
L=len(setlist)
Lset=windowsize #juste for speed writing
print(L)
thematrix=np.zeros((L,L))
i=0
j=0
print("====>Creation de la matrice")
print(thematrix.shape)
while i<L:
while j<L:
if j>i:
commonL=len(setlist[i].intersection(setlist[j]))
Li=sizelist[i]
Lj=sizelist[j]
val=commonL-max((Li-Lj),(Lj-Li))
thematrix[i,j]=val
thematrix[j,i]=val
j+=1
j=0
i+=1
print("====>Dumping de la matrice")
#matlabdict={}#just to be un matlab savemat format
#matlabdict['mat']=thematrix #not need sparse: not so many 0
#scpio.savemat(dumpmatname,matlabdict)
pickle.dump(thematrix,open(dumpmatname,"wb")) #other option of dump but with bigger file
print("===> Afichage de la matrice")
manipname=repository+achr+endofthefile+"recurenceplot.png"
print(thematrix.shape)
print(np.where(thematrix<0))
utils.showamatwithcolorcode(np.add(thematrix,1),manipname,"bwr") #jet<bwr
return thematrix
