def Run2( flist ):
aps = AllPossStrings( 'ACGT',7)
NF = len( flist ) # the number of files
for i in range( NF ):
print 'Working on ',flist[i]
# get the data
dna = fasta.Fasta( 'bacteria/' + flist[i] )
# count the number of genes
NG = len( dna )
# if there are multiple genes then combine
if NG >1:
t = []
for j in range( NG ):
t.append( dna[j][1] )
st = ''.join(t)
del t
else:
st = dna[0][1]
del dna
# for every million bases make a plot
NP = int(len( st )/1000000)
#if NP > 3:
#NP = 3
for j in range( NP ):
print '\tPortion',j,'of',NP
ctr = Counter( aps, st[j*1000000:j*1000000+1000000] )
akando.a2i( ctr ).save('work/chaos'+str(i)+'c'+str(j)+'.gif' )
def Run2(flist):
aps = AllPossStrings('ACGT', 7)
NF = len(flist) # the number of files
for i in range(NF):
print 'Working on ', flist[i]
# get the data
dna = fasta.Fasta('bacteria/' + flist[i])
# count the number of genes
NG = len(dna)
# if there are multiple genes then combine
if NG > 1:
t = []
for j in range(NG):
t.append(dna[j][1])
st = ''.join(t)
del t
else:
st = dna[0][1]
del dna
# for every million bases make a plot
NP = int(len(st) / 1000000)
#if NP > 3:
#NP = 3
for j in range(NP):
print '\tPortion', j, 'of', NP
ctr = Counter(aps, st[j * 1000000:j * 1000000 + 1000000])
akando.a2i(ctr).save('work/chaos' + str(i) + 'c' + str(j) + '.gif')
def MakeColorPic(mmb, data):
pic = zeros((512, 512, 3), int)
NC = len(mmb) # number of clusters = number of colors
for i in range(NC):
# for each color
for j in mmb[i]:
x, y = (data[j] + 1) * 240
x, y = int(x), int(y)
pic[x, y, 0] = 250 - 250 / NC * i # red
if i > 150: pic[x, y, 1] = (i - 150) * 20 # green
pic[x, y, 2] = i * 250 # blue
r = akando.a2i(pic[:, :, 0])
g = akando.a2i(pic[:, :, 1])
b = akando.a2i(pic[:, :, 2])
mg = Image.merge('RGB', (r, g, b))
return mg
def Color4( net ):
# net from Make SOM
# convert 4 channels to 3colors
V,H,N = net.shape
red = zeros( (V,H), float )
green = zeros( (V,H), float )
# first channel
blue = net[:,:,0] + 0.67*net[:,:,1] + 0.33*net[:,:,2]
green = 0.1*net[:,:,0] + 0.4*net[:,:,1] + 0.4*net[:,:,2]+0.1*net[:,:,3]
red = net[:,:,3] + 0.67*net[:,:,2] + 0.33*net[:,:,1]
#
r = akando.a2i( red )
g = akando.a2i( green )
b = akando.a2i( blue )
mg = Image.merge( 'RGB', (r,g,b) )
return mg
def MakeColorPic( mmb, data ):
pic = zeros( (512,512,3), int )
NC = len( mmb ) # number of clusters = number of colors
for i in range( NC ):
# for each color
for j in mmb[i]:
x,y = (data[j]+1)*240
x,y = int(x), int(y)
pic[x,y,0] = 250 - 250/NC*i # red
if i>150: pic[x,y,1] = (i-150) *20 # green
pic[x,y,2] = i*250 # blue
r = akando.a2i( pic[:,:,0] )
g = akando.a2i( pic[:,:,1] )
b = akando.a2i( pic[:,:,2] )
mg = Image.merge( 'RGB', (r,g,b) )
return mg
def MakePic(data):
# assume that the maximum radius of the data is 1
pic = zeros((512, 512), int)
for i in data:
x, y = (i + 1) * 240
pic[int(x), int(y)] += 1
mg = akando.a2i(pic)
return mg
def MakePic( data ):
# assume that the maximum radius of the data is 1
pic = zeros( (512,512), int )
for i in data:
x,y = (i+1)*240
pic[ int(x), int(y)] +=1
mg = akando.a2i( pic )
return mg
def Color4(net):
# net from Make SOM
# convert 4 channels to 3colors
V, H, N = net.shape
red = zeros((V, H), float)
green = zeros((V, H), float)
# first channel
blue = net[:, :, 0] + 0.67 * net[:, :, 1] + 0.33 * net[:, :, 2]
green = 0.1 * net[:, :, 0] + 0.4 * net[:, :,
1] + 0.4 * net[:, :,
2] + 0.1 * net[:, :,
3]
red = net[:, :, 3] + 0.67 * net[:, :, 2] + 0.33 * net[:, :, 1]
#
r = akando.a2i(red)
g = akando.a2i(green)
b = akando.a2i(blue)
mg = Image.merge('RGB', (r, g, b))
return mg
def Run1():
data = genbank.ReadGenbank( '/science/bartlett/genbank/nc_00918.gb.txt')
dna = genbank.ParseDNA( data )
aps = AllPossStrings( 'cgat' )
ctr = Counter( aps, dna )
akando.a2i( ctr ).save('dud.gif')
def Run1():
data = genbank.ReadGenbank('/science/bartlett/genbank/nc_00918.gb.txt')
dna = genbank.ParseDNA(data)
aps = AllPossStrings('cgat')
ctr = Counter(aps, dna)
akando.a2i(ctr).save('dud.gif')
def SOMmg( som ):
r = akando.a2i( som[:,:,0] )
g = akando.a2i( som[:,:,1] )
b = akando.a2i( som[:,:,2] )
mg = Image.merge( 'RGB', (r,g,b) )
return mg
def SOMmg(som):
r = akando.a2i(som[:, :, 0])
g = akando.a2i(som[:, :, 1])
b = akando.a2i(som[:, :, 2])
mg = Image.merge('RGB', (r, g, b))
return mg