def __init__(self,probfile,nucleusRadius=5000.0,contactRange=1,level=None,record=-1):
self.probmat = matrix.contactmatrix(probfile)
self.nbead = len(self.probmat)
#setup log
LEVELS={'debug':logging.DEBUG,'info':logging.INFO,'warning':logging.WARNING,'error':logging.ERROR,'critical':logging.CRITICAL}
loglevel = LEVELS.get(level,logging.NOTSET)
self.logger = logging.getLogger()
self.logger.setLevel(loglevel)
self._log_capture_string = StringIO()
chhandler = logging.StreamHandler(self._log_capture_string)
chhandler.setLevel(loglevel)
self.logger.addHandler(chhandler)
self.logger.setLevel(loglevel)
#setup record
self._record_step = record
if record >= 100:
self.record = []
#CONST
rscale = 1.38 # 20% occupancy
self.nucleusRadius = nucleusRadius # nm
cdensity = 107.45 # bp/nm assuming 197 bp/nucleosomes and 6 nucleosome/11 nm
kscale = (0.75*15**2)**(1.0/3.0) # 3/4*r**2 where r=15nm
self.contactRange = contactRange # surface to surface distance scale of (r1+r2)
# for which 2 beads are considered as contact
#get radius of each bead
self.beadRadius = [rscale * kscale * ((index['end'] - index['start'])/cdensity) ** (1.0/3.0) for index in self.probmat.idx]
#calculate the total volumn of DNA (diploid) and nucleus
dnavol = sum(4. * 3.1415/3. * np.array(self.beadRadius)**3) * 2
nucvol = (4*3.1415/3)*self.nucleusRadius**3
#And chromosome occupancy
dnaocc = dnavol / nucvol
self.logger.debug('occupancy: %.2f with Rnuc %d'%(dnaocc,self.nucleusRadius))
#diploid Rb; 2xtotal haploid beads
self.beadRadius = self.beadRadius + self.beadRadius
# Chromosome territory apply
self.genome = utils.genome(self.probmat.genome)
cscale=1.0
chrvol = nucvol * self.genome.info['length']/sum(self.genome.info['length'])/2
self.chromRadius=cscale*((chrvol/4*3/3.1415)**(1./3.))
#record starting time
self.model = IMP.Model()
self.chain = IMP.container.ListSingletonContainer(self.model)
self.restraints = IMP.RestraintSet(self.model)
#IMP.set_check_level(IMP.USAGE)
IMP.set_check_level(IMP.NONE)
IMP.set_log_level(IMP.SILENT)
#setup nucleus envelope
self.center = IMP.algebra.Vector3D(0,0,0)
def getContactMap(self,contactRange=1):
"""
Return contact matrix format contact heatmap
"""
from scipy.spatial import distance
modelmap = matrix.contactmatrix(self.nbead)
modelmap.idx = copy.deepcopy(self.idx)
modelmap.genome = copy.deepcopy(self.genome)
modelmap.resolution = None
n = self.nbead*2
dcap = distance.cdist(self.radius,-self.radius)*(contactRange+1)
cmap = np.zeros((n,n))
for i in range(self.nstruct):
if (i+1)*10.0 % self.nstruct == 0:
print("%.3f %%"%((i+1)*100.0 / self.nstruct))
#print(i)
dist = distance.cdist(self.coordinates[i],self.coordinates[i],'euclidean')
submap = dist <= dcap
cmap += submap
modelmap.matrix = cmap[:n/2,:n/2]+cmap[:n/2,n/2:]+cmap[n/2:,:n/2]+cmap[n/2:,n/2:]
modelmap.matrix = modelmap.matrix/self.nstruct/2
return modelmap
def getContactMap(self,contactRange=1):
"""
Return contact matrix format contact heatmap
"""
from scipy.spatial import distance
modelmap = matrix.contactmatrix(self.nbead)
modelmap.idx = copy.deepcopy(self.idx)
modelmap.genome = copy.deepcopy(self.genome)
modelmap.resolution = None
n = self.nbead*2
dcap = distance.cdist(self.radius,-self.radius)*(contactRange+1)
cmap = np.zeros((n,n))
for i in range(self.nstruct):
if (i+1)*10.0 % self.nstruct == 0:
print("%.3f %%"%((i+1)*100.0 / self.nstruct))
#print(i)
dist = distance.cdist(self.coordinates[i],self.coordinates[i],'euclidean')
submap = dist <= dcap
cmap += submap
modelmap.matrix = cmap[:n/2,:n/2]+cmap[:n/2,n/2:]+cmap[n/2:,:n/2]+cmap[n/2:,n/2:]
modelmap.matrix = modelmap.matrix/self.nstruct/2
return modelmap
def __init__(self,
probfile,
nucleusRadius=5000.0,
chromosomeOccupancy=0.2,
contactRange=1,
level=None):
self.probmat = alabmatrix.contactmatrix(probfile)
self.nbead = len(self.probmat)
#setup log
LEVELS = {
'debug': logging.DEBUG,
'info': logging.INFO,
'warning': logging.WARNING,
'error': logging.ERROR,
'critical': logging.CRITICAL
}
loglevel = LEVELS.get(level, logging.NOTSET)
self.logger = logging.getLogger()
self.logger.setLevel(loglevel)
self._log_capture_string = io.StringIO()
chhandler = logging.StreamHandler(self._log_capture_string)
chhandler.setLevel(loglevel)
self.logger.addHandler(chhandler)
self.logger.setLevel(loglevel)
#CONST
#rscale = 1.38 # 20% occupancy
self.occupancy = chromosomeOccupancy #chromosome occupancy in nucleus, defined as diploid_domain_total_volume/nuclear_volume
self.nucleusRadius = nucleusRadius # nm
#cdensity = 107.45 # bp/nm assuming 197 bp/nucleosomes and 6 nucleosome/11 nm
#kscale = (0.75*15**2)**(1.0/3.0) # 3/4*r**2 where r=15nm
self.contactRange = contactRange # surface to surface distance scale of (r1+r2)
# for which 2 beads are considered as contact
self.genome = alabutils.genome(self.probmat.genome)
rho = self.occupancy * self.nucleusRadius**3 / (
2 * sum(self.genome.info['length']))
#get radius of each bead
self.beadRadius = [(rho * (index['end'] - index['start']))**(1.0 / 3.0)
for index in self.probmat.idx]
#self.beadRadius = [rscale * kscale * ((index['end'] - index['start'])/cdensity) ** (1.0/3.0) for index in self.probmat.idx]
#calculate the total volumn of DNA (diploid) and nucleus
dnavol = sum(4. * 3.1415 / 3. * np.array(self.beadRadius)**3) * 2
nucvol = (4 * 3.1415 / 3) * self.nucleusRadius**3
#And chromosome occupancy
dnaocc = dnavol / nucvol
self.logger.debug(u'Occupancy: %.2f with Rnuc %d' %
(dnaocc, self.nucleusRadius))
#diploid Rb; 2xtotal haploid beads
self.beadRadius = self.beadRadius + self.beadRadius
# Chromosome territory apply
#self.genome = alabutils.genome(self.probmat.genome)
cscale = 1.0
chrvol = nucvol * self.genome.info['length'] / sum(
self.genome.info['length']) / 2
self.chromRadius = cscale * ((chrvol / 4 * 3 / 3.1415)**(1. / 3.))
#record starting time
self.model = IMP.Model()
self.chain = IMP.container.ListSingletonContainer(self.model)
self.restraints = IMP.RestraintSet(self.model)
#IMP.set_check_level(IMP.USAGE)
IMP.set_check_level(IMP.NONE)
IMP.set_log_level(IMP.SILENT)
#setup nucleus envelope
self.center = IMP.algebra.Vector3D(0, 0, 0)