def _generate_throats(self):
r"""
Generate the throats (connections, numbering and types)
"""
Nx = self._Nx
Ny = self._Ny
Nz = self._Nz
Np = Nx * Ny * Nz
ind = sp.arange(0, Np)
#Generate throats based on pattern of the adjacency matrix
tpore1_1 = ind[(ind % Nx) < (Nx - 1)]
tpore2_1 = tpore1_1 + 1
tpore1_2 = ind[(ind % (Nx * Ny)) < (Nx * (Ny - 1))]
tpore2_2 = tpore1_2 + Nx
tpore1_3 = ind[(ind % Np) < (Nx * Ny * (Nz - 1))]
tpore2_3 = tpore1_3 + Nx * Ny
tpore1 = sp.hstack((tpore1_1, tpore1_2, tpore1_3))
tpore2 = sp.hstack((tpore2_1, tpore2_2, tpore2_3))
connections = sp.vstack((tpore1, tpore2)).T
connections = connections[sp.lexsort(
(connections[:, 1], connections[:, 0]))]
self['throat.all'] = sp.ones_like(sp.arange(0,
sp.shape(tpore1)[0]),
dtype=bool)
self['throat.conns'] = connections
def unique(a):
order = sp.lexsort(a.T)
a = a[order]
diff = sp.diff(a, axis=0)
ui = sp.ones(len(a), 'bool')
ui[1:] = (diff != 0).any(axis=1)
return a[ui]
def simplex_array_boundary(s, parity):
"""
Compute the boundary faces and boundary operator of an
array of simplices with given simplex parities
E.g.
For a mesh with two triangles [0,1,2] and [1,3,2], the second
triangle has opposite parity relative to sorted order.
simplex_array_boundary(array([[0,1,2],[1,2,3]]),array([0,1]))
"""
#TODO handle edge case as special case
num_simplices = s.shape[0]
faces_per_simplex = s.shape[1]
num_faces = num_simplices * faces_per_simplex
orientations = 1 - 2 * parity
#faces[:,:-2] are the indices of the faces
#faces[:,-2] is the index of the simplex whose boundary produced the face
#faces[:,-1] is the orientation of the face in the boundary of the simplex
faces = empty((num_faces, s.shape[1] + 1), dtype=s.dtype)
for i in range(faces_per_simplex):
rows = faces[num_simplices * i:num_simplices * (i + 1)]
rows[:, :i] = s[:, :i]
rows[:, i:-2] = s[:, i + 1:]
rows[:, -2] = arange(num_simplices)
rows[:, -1] = ((-1)**i) * orientations
#sort rows
faces = faces[lexsort(faces[:, :-2].T[::-1])]
#find unique faces
face_mask = ~hstack(
(array([False]), alltrue(faces[1:, :-2] == faces[:-1, :-2], axis=1)))
unique_faces = faces[face_mask, :-2]
#compute CSR representation for boundary operator
csr_indptr = hstack((arange(num_faces)[face_mask], array([num_faces])))
csr_indices = ascontiguousarray(faces[:, -2])
csr_data = faces[:, -1].astype('int8')
shape = (len(unique_faces), num_simplices)
boundary_operator = csr_matrix((csr_data, csr_indices, csr_indptr), shape)
return unique_faces, boundary_operator
def simplex_array_boundary(s,parity):
"""
Compute the boundary faces and boundary operator of an
array of simplices with given simplex parities
E.g.
For a mesh with two triangles [0,1,2] and [1,3,2], the second
triangle has opposite parity relative to sorted order.
simplex_array_boundary(array([[0,1,2],[1,2,3]]),array([0,1]))
"""
#TODO handle edge case as special case
num_simplices = s.shape[0]
faces_per_simplex = s.shape[1]
num_faces = num_simplices * faces_per_simplex
orientations = 1 - 2*parity
#faces[:,:-2] are the indices of the faces
#faces[:,-2] is the index of the simplex whose boundary produced the face
#faces[:,-1] is the orientation of the face in the boundary of the simplex
faces = empty((num_faces,s.shape[1]+1),dtype=s.dtype)
for i in range(faces_per_simplex):
rows = faces[num_simplices*i:num_simplices*(i+1)]
rows[:, : i] = s[:, :i]
rows[:,i :-2] = s[:,i+1: ]
rows[:, -2 ] = arange(num_simplices)
rows[:, -1 ] = ((-1)**i)*orientations
#sort rows
faces = faces[lexsort( faces[:,:-2].T[::-1] )]
#find unique faces
face_mask = -hstack((array([False]),alltrue(faces[1:,:-2] == faces[:-1,:-2],axis=1)))
unique_faces = faces[face_mask,:-2]
#compute CSR representation for boundary operator
csr_indptr = hstack((arange(num_faces)[face_mask],array([num_faces])))
csr_indices = ascontiguousarray(faces[:,-2])
csr_data = faces[:,-1].astype('int8')
shape = (len(unique_faces),num_simplices)
boundary_operator = csr_matrix((csr_data,csr_indices,csr_indptr), shape)
return unique_faces,boundary_operator
def sort_rows(array, index=None):
"""Sort array by rows"""
if array.shape[0] == 0:
if index == True:
return (array, [])
else:
return (array)
s_idx = sp.lexsort([array[:, -i] for i in range(1, array.shape[1] + 1)])
if index == True:
return (array[s_idx, :], s_idx)
else:
return array[s_idx, :]
def sort_rows(array, index = None):
"""Sort array by rows"""
if array.shape[0] == 0:
if index == True:
return (array, [])
else:
return (array)
s_idx = sp.lexsort([array[:, -i] for i in range(1, array.shape[1] + 1)])
if index == True:
return (array[s_idx, :], s_idx)
else:
return array[s_idx, :]
def _generate_throats(self):
r"""
Generate the throats (connections, numbering and types)
"""
Nx = self._Nx
Ny = self._Ny
Nz = self._Nz
Np = Nx*Ny*Nz
ind = sp.arange(0,Np)
#Generate throats based on pattern of the adjacency matrix
tpore1_1 = ind[(ind%Nx)<(Nx-1)]
tpore2_1 = tpore1_1 + 1
tpore1_2 = ind[(ind%(Nx*Ny))<(Nx*(Ny-1))]
tpore2_2 = tpore1_2 + Nx
tpore1_3 = ind[(ind%Np)<(Nx*Ny*(Nz-1))]
tpore2_3 = tpore1_3 + Nx*Ny
tpore1 = sp.hstack((tpore1_1,tpore1_2,tpore1_3))
tpore2 = sp.hstack((tpore2_1,tpore2_2,tpore2_3))
connections = sp.vstack((tpore1,tpore2)).T
connections = connections[sp.lexsort((connections[:, 1], connections[:, 0]))]
self['throat.all'] = sp.ones_like(sp.arange(0,sp.shape(tpore1)[0]),dtype=bool)
self['throat.conns'] = connections
def simplex_array_searchsorted(s, v):
"""Find the row indices (of s) corresponding to the simplices stored
in the rows of simplex array v. The rows of s must be stored in
lexicographical order.
Example
-------
>>> from numpy import array
>>> s = array([[0,1],[0,2],[1,2],[1,3]])
>>> v = array([[1,2],[0,2]])
>>> simplex_array_searchsorted(s,v)
array([2, 1])
"""
s = asarray(s)
v = asarray(v)
if ndim(s) != 2 or ndim(v) != 2:
raise ValueError('expected rank 2 arrays')
if s.shape[1] != v.shape[1]:
raise ValueError('number of columns must agree')
# compute row indices by sorting both arrays together
Ns = s.shape[0]
Nv = v.shape[0]
perm = lexsort(vstack((s, v))[:, ::-1].T)
flags = concatenate((ones(Ns, dtype=int), zeros(Nv, dtype=int)))
indices = empty(Ns + Nv, dtype=int)
indices[perm] = cumsum(flags[perm])
indices = indices[Ns:].copy()
indices -= 1
return indices
def simplex_array_searchsorted(s, v):
"""Find the row indices (of s) corresponding to the simplices stored
in the rows of simplex array v. The rows of s must be stored in
lexicographical order.
Example
-------
>>> from numpy import array
>>> s = array([[0,1],[0,2],[1,2],[1,3]])
>>> v = array([[1,2],[0,2]])
>>> simplex_array_searchsorted(s,v)
array([2, 1])
"""
s = asarray(s)
v = asarray(v)
if rank(s) != 2 or rank(v) != 2:
raise ValueError('expected rank 2 arrays')
if s.shape[1] != v.shape[1]:
raise ValueError('number of columns must agree')
# compute row indices by sorting both arrays together
Ns = s.shape[0]
Nv = v.shape[0]
perm = lexsort(vstack((s,v))[:,::-1].T)
flags = concatenate( (ones(Ns,dtype=int),zeros(Nv,dtype=int)) )
indices = empty(Ns+Nv, dtype=int)
indices[perm] = cumsum(flags[perm])
indices = indices[Ns:].copy()
indices -= 1
return indices
def processMultiTranscriptGenes(tcrpts):
### all transcript isoforms have at least two exons
if sp.sum(np.core.defchararray.find(tcrpts,',') != -1) != len(tcrpts):
return None
#### make matrix of transcript struc and length
myExons = [x.split(':')[1].split(',') for x in tcrpts]
myExons = sp.array([reduce(lambda x, y: x + y, myExons)]).ravel() ### unravel exons into one list of exons
myExonsInt = sp.array([x.split('-') for x in myExons]).astype('int')
### sort this
sidxInt = sp.lexsort((myExonsInt[:,1], myExonsInt[:,0]))
myExons = myExons[sidxInt]
myExonsInt = myExonsInt[sidxInt,:]
### see how often i got each item
dummy, uidx, dists = ut.unique_rows(myExonsInt, index=True, counts = True)
N_match = sp.sum(dists == len(tcrpts))
if N_match < 3: ### i want at lest 3 constitutive exons
return None
### get constitutitve exons
iConst = dists == len(tcrpts)
uqConstEx = myExons[uidx][iConst]
firstEx = uqConstEx[0]
lastEx = uqConstEx[-1]
## get length of all transcripts
myExStrucL = []
for i,rec in enumerate(tcrpts):
myExStrucL.append(getTranscriptLengthBex(rec, firstEx, lastEx))
firstEx = tcrpts[0].split(':')[0] + ':' + firstEx + ':' + tcrpts[0].split(':')[2]
lastEx = tcrpts[0].split(':')[0] + ':' + lastEx + ':' + tcrpts[0].split(':')[2]
return [firstEx, lastEx, tcrpts[0].split(':')[0],tcrpts[0].split(':')[2], str(sp.median(myExStrucL))]
def sort_rows(array, index = None):
"""Sort array by rows"""
### empty array
if array.shape[0] == 0:
if index == True:
return (array, [])
else:
return (array)
### only one row
if len(array.shape) == 1:
if index == True:
return (array, [0])
else:
return (array)
### more than one row
s_idx = sp.lexsort([array[:, -i] for i in range(1, array.shape[1] + 1)])
if index == True:
return (array[s_idx, :], s_idx)
else:
return array[s_idx, :]
def sort_rows(array, index=None):
"""Sort array by rows"""
### empty array
if array.shape[0] == 0:
if index == True:
return (array, [])
else:
return (array)
### only one row
if len(array.shape) == 1:
if index == True:
return (array, [0])
else:
return (array)
### more than one row
s_idx = sp.lexsort([array[:, -i] for i in range(1, array.shape[1] + 1)])
if index == True:
return (array[s_idx, :], s_idx)
else:
return array[s_idx, :]
def _generate_throats(self):
r"""
Generate the throats (connections, numbering and types)
"""
self._logger.info("generate_throats: Define connections between pores")
[Nx, Ny, Nz] = sp.shape(self._template)
Np = Nx*Ny*Nz
ind = np.arange(0, Np)
#Generate throats based on pattern of the adjacency matrix
#This is taken from Cubic
tpore1_1 = ind[(ind % Nx) < (Nx-1)]
tpore2_1 = tpore1_1 + 1
tpore1_2 = ind[(ind % (Nx*Ny)) < (Nx*(Ny-1))]
tpore2_2 = tpore1_2 + Nx
tpore1_3 = ind[(ind % Np) < (Nx*Ny*(Nz-1))]
tpore2_3 = tpore1_3 + Nx*Ny
tpore1 = sp.hstack((tpore1_1, tpore1_2, tpore1_3))
tpore2 = sp.hstack((tpore2_1, tpore2_2, tpore2_3))
connections = sp.vstack((tpore1, tpore2)).T
connections = connections[sp.lexsort((connections[:, 1], connections[:, 0]))]
#Remove throats to non-active pores
img_ind = self.get_pore_data(prop='voxel_index')
temp0 = sp.in1d(connections[:, 0], img_ind)
temp1 = sp.in1d(connections[:, 1], img_ind)
tind = temp0*temp1
connections = connections[tind]
#Need a cleaner way to do this other than voxel_to_pore map...figure out later
self.set_throat_data(prop='connections', data=self._voxel_to_pore_map[connections])
self.set_throat_info(label='all', locations=sp.ones(sp.sum(tind,),dtype=bool))
self.set_throat_data(prop='numbering', data=np.arange(0, sp.sum(tind)))
self._logger.debug("generate_throats: End of method")
def readExpDataBam(base_dir):
# base_dir = "/cbio/grlab/projects/TCGA/PanCancer/icgc_qc"
allfiles = os.listdir(base_dir)
allfiles = fnmatch.filter(allfiles, '*.tsv')
for i,f in enumerate(allfiles):
if i == 0:
header = sp.array([f.split('.')[0]])
data = sp.array(pandas.read_csv(os.path.join(base_dir, f), delim_whitespace = True))#sp.loadtxt(os.path.join(base_dir, f), delimiter = '\t', dtype = 'string')
exonpos = data[:,0]#data[:,[0,1]].ravel('C')
data = data[:,1].astype('float')#data[:,[6,7]].ravel('C').astype('float')
else:
header = sp.hstack((header, sp.array([f.split('.')[0]])))
tmp = sp.array(pandas.read_csv(os.path.join(base_dir, f), delim_whitespace = True))#sp.loadtxt(os.path.join(base_dir, f), delimiter = '\t', dtype = 'string')
tmp = tmp[:,1].astype('float')#tmp[:,[6,7]].ravel('C').astype('float')
data = sp.vstack((data, tmp))
if len(data.shape) == 1:
data = data[:, sp.newaxis]
else:
data = data.T
sidx = sp.argsort(header)
header = header[sidx]
data = data[:, sidx]
### remove non chromosomal contigs
iOK = sp.array([x.startswith('chr') for x in exonpos])
exonpos = exonpos[iOK]
data = data[iOK,:]
chrm = sp.array([x.split(':')[0].strip('chr') for x in exonpos])
start = sp.array([x.split(':')[1].split('-')[0] for x in exonpos]).astype('int')
sidx = sp.lexsort((start, chrm))
exonpos = exonpos[sidx]
data = data[sidx,:]
return exonpos, header, data
def sort(self):
s_idx = sp.lexsort([self.vertices[1, :], self.vertices[0, :]])
self.reorder(s_idx)
def getOverlapGenes(fn, format):
"""
Returns a list of gene names which are overlapping
"""
### Read gene annotation from gaf
data = []
if format == 'gaf':
for l in open(fn, 'r'):
lSpl = l.strip('\n').split('\t')
if lSpl[2] != 'gene':
continue
if lSpl[8] != 'genome':
continue
if lSpl[15] == '':
continue
data.append([lSpl[1],lSpl[16]])
elif format == 'gtf':
for l in open(fn, 'r'):
## comments
if l[0] == '#':
continue
lSpl = l.strip('\n').split('\t')
if lSpl[2].lower() != 'gene':
continue
tags = get_tags_gtf(lSpl[8])
data.append([tags['gene_id'], '%s:%s-%s' % (lSpl[0], lSpl[3], lSpl[4])])
elif format in ['gff', 'gff3']:
for l in open(fn, 'r'):
## comments
if l[0] == '#':
continue
lSpl = l.strip('\n').split('\t')
if not lSpl[2].lower() in ['gene', 'lincrna_gene', 'mirna_gene', 'processed_transcript', 'rrna_gene', 'snrna_gene', 'snorna_gene']:
continue
tags = get_tags_gff3(lSpl[8])
try:
data.append([tags['ID'], '%s:%s-%s' % (lSpl[0], lSpl[3], lSpl[4])])
except KeyError:
data.append([tags['Parent'], '%s:%s-%s' % (lSpl[0], lSpl[3], lSpl[4])])
### data contains two o columns: gene_ID, GeneLocus (e.g., chr7:130020290-130027948:+)
data = sp.array(data)
### fix positions
pos = data[:,1]
pos = sp.array([x.split(':')[0]+'-'+x.split(':')[1] for x in pos])
pos = sp.array([x.strip('chr') for x in pos])
pos = sp.array([x.split('-') for x in pos])
pos[pos[:,0] == 'X',0] = '23'
pos[pos[:,0] == 'Y',0] = '24'
### filter weird things like mitochondria etc.
iOK = np.core.defchararray.isdigit(pos[:,0])
pos = pos[iOK,:]
data = data[iOK,:]
pos = pos.astype('int')
### sort everything nicely
sidx = sp.lexsort((pos[:,2], pos[:,1], pos[:,0]))
pos = pos[sidx,:]
data = data[sidx,:]
### find genes with overlapping annotations
myOverlapGenes = []
for i in xrange(pos.shape[0]):
mypos = pos[i,:]
## same chr
iChr = mypos[0] == pos[:,0]
## end is in something else
iLBEnd = mypos[2] >= pos[:,1]
iUBEnd = mypos[2] <= pos[:,2]
## st is in something else
iLBSt = mypos[1] <= pos[:,2]
iUBSt = mypos[1] >= pos[:,1]
## on both ends the only entry that overlaps to i is i itself --> continue
if (sp.sum(iChr & iLBEnd & iUBEnd) == 1) and (sp.sum(iChr & iLBSt & iUBSt) == 1):
continue
### extract IDs of overlapping genes
overlapgenesSt = data[iChr & iUBSt & iLBSt, 0]
overlapgenesEnd = data[iChr & iUBEnd & iLBEnd, 0]
overlapgenesSt = sp.array([x.split('|')[0] for x in overlapgenesSt])
overlapgenesEnd = sp.array([x.split('|')[0] for x in overlapgenesEnd])
### this shoudl actually never happen ...
if (sp.unique(overlapgenesSt).shape[0] == 1) and (sp.unique(overlapgenesEnd).shape[0] == 1):
continue
if sp.unique(overlapgenesSt).shape[0] > 1:
myOverlapGenes.extend(overlapgenesSt.tolist())
if sp.unique(overlapgenesEnd).shape[0] > 1:
myOverlapGenes.extend(overlapgenesEnd.tolist())
return sp.unique(myOverlapGenes)
