def saveByChromosomeHeatmap(self,
filename,
resolution,
gInfo,
includeTrans=False):
self.genome.setResolution(resolution)
mydict = h5dict(filename)
for chrom in range(self.genome.chrmCount):
c1 = self.h5dict.get_dataset("chrms1")
p1 = self.h5dict.get_dataset("cuts1")
low = h5dictBinarySearch(c1, p1, (chrom, -1), "left")
high = h5dictBinarySearch(c1, p1, (chrom, 999999999), "right")
chr1 = self._getVector("chrms1", low, high)
chr2 = self._getVector("chrms2", low, high)
pos1 = np.array(self._getVector("mids1", low, high) // resolution,
dtype=np.int32)
pos2 = np.array(self._getVector("mids2", low, high) // resolution,
dtype=np.int32)
assert (chr1 == chrom).all() # getting sure that bincount worked
args = np.argsort(chr2)
chr2 = chr2[args]
pos1 = pos1[args]
pos2 = pos2[args]
for chrom2 in range(chrom, self.genome.chrmCount):
if (includeTrans == False) and (chrom2 != chrom):
continue
start = np.searchsorted(chr2, chrom2, "left")
end = np.searchsorted(chr2, chrom2, "right")
cur1 = pos1[start:end]
cur2 = pos2[start:end]
label = np.array(cur1, "int64")
label *= self.genome.chrmLensBin[chrom2]
label += cur2
maxLabel = self.genome.chrmLensBin[chrom] * \
self.genome.chrmLensBin[chrom2]
counts = np.bincount(label, minlength=maxLabel)
mymap = counts.reshape((self.genome.chrmLensBin[chrom], -1))
if chrom == chrom2:
mymap = mymap + mymap.T
fillDiagonal(mymap, np.diag(mymap).copy() / 2)
mydict["%d %d" % (chrom, chrom2)] = mymap
mydict['resolution'] = resolution
mydict['genomeInformation'] = gInfo
return
desierd_fragids = []
c1_h5 = fragments.h5dict.get_dataset("chrms1")
p1_h5 = fragments.h5dict.get_dataset("cuts1")
c2_h5 = fragments.h5dict.get_dataset("chrms2")
p2_h5 = fragments.h5dict.get_dataset("cuts2")
for ind, region in enumerate(regions):
chrm, st, end = region
chrm = chrm[
1:] #Stupid names: in genome_db they are T_nnnn due to chrmFileTemplate="N%s.fa", but normally they are NT_nnnn.
if not chrm in genome_db.label2idx.keys():
continue
else:
chrm = genome_db.label2idx[chrm]
low1 = h5dictBinarySearch(c1_h5, p1_h5, (chrm, st), "left")
high1 = h5dictBinarySearch(c1_h5, p1_h5, (chrm, end), "right")
if low1 != high1:
desierd_fragids += list(
np.unique(fragments._getVector("fragids1", low1,
high1)))
low2 = h5dictBinarySearch(c2_h5, p2_h5, (chrm, st), "left")
high2 = h5dictBinarySearch(c2_h5, p2_h5, (chrm, end), "right")
if low2 != high2:
desierd_fragids += list(
np.unique(fragments._getVector("fragids1", low2,
high2)))
desierd_fragids = np.unique(desierd_fragids)
print len(desierd_fragids) #DEBUG