def cycles_vs_align_len(classData, blastPath, floworder):
pylab.clf()
l = []
c = []
for rowcol,leng,dif,seq in classData:
t = template.deseqify(remove_spaces(seq), floworder)
l.append(dif)
c.append(len(t)/4)
pylab.scatter(l,c)
if "/" in blastPath:
p = blastPath.strip().split("/")[-1]
path = p.strip().split(".")[0]
else:
path = blastPath.strip().split(",")[0]
if 'blastn' in path:
pretitle = 'Relaxed Blast'
if 'megablast' in path:
pretitle = 'Strict Blast'
pylab.title("%s Number of Flows vs. Alignment Length" % pretitle)
pylab.xlabel("Length")
pylab.ylabel("Flows")
pylab.gcf().set_size_inches((8,4))
pylab.axis([0,max(l)+10,0,max(c)+10])
#x = [2.2*i for i in range(max(l))]
#pylab.plot(x)
pylab.savefig("alignment_vs_cycles_%s.png" % path)
pylab.clf()
def get_ionograms(rowCollist, outfolder, alignmenthtml, sffIn, alignstringfill, byLength, space_string, key, floworder):
filelist = {}
alignhtml = {}
for i in rowCollist:
rowcol = i[0]
row = rowcol[0]
col = rowcol[1]
fin = Popen("SFFRead %s -C %s -R %s" % (sffIn,col,row), shell=True, stdout=PIPE)
ionogram = fin.stdout.read()
ionogram = ionogram.strip()
ionogram = ionogram.split(" ")
ionogram = [float(i) for i in ionogram]
s = alignstringfill[rowcol][0]
expected = []
lenOfIon = len(ionogram)
l = length(str(s.strip()))
alignhtml[rowcol] = check_for_alignment(ionogram, alignstringfill, rowcol, floworder, key)
fskey = template.deseqify(key, floworder)
expected = fskey + list(pylab.zeros(lenOfIon-len(fskey)))
intexp = []
for i in expected:
intexp.append(int(i))
expected = intexp
titleString = 'Single-Well Ionogram for (%s,%s) Length=%s Bases' % (int(row), int(col), l)
it = plotters.IonogramJMR(floworder, expected[:len(ionogram)],ionogram,titleString)
it.render()
filelist[rowcol] = ("Well_(%s,%s).png" % (int(row),int(col)))
pylab.savefig(outfolder + "/Well_(%s,%s).png" % (int(row),int(col)))
generateWeb(alignhtml, filelist, outfolder, space_string, rowCollist)
def plot(self):
num = 1
numGraphs = math.ceil(math.sqrt(self.get_num_graphs()))
Rows = int(numGraphs)
Cols = int(numGraphs)
pylab.clf()
fig = pylab.figure(1, figsize=(Rows, Cols))
flowspacekey = template.deseqify(self.key[: len(self.key) - 1], self.floworder)
flowspacekey = flowspacekey[: len(flowspacekey) - 1]
for region, data in self.data.iteritems():
# ATCG 01001011
trace = {}
flowstring = [self.floworder[n % len(self.floworder)] for n in range(len(flowspacekey))]
flowstring = "".join(flowstring)
flowstring = flowstring
for n, base in enumerate(list(self.floworder)):
baseIndexs = self.getindex(base, flowstring)
min = None
max = []
for i in baseIndexs:
mer = flowspacekey[i]
if mer == 0:
if min == None: # only take first zero of any nuc for subtraction
min = data[i]
if mer == 1:
max.append(data[i])
if len(max) > 0 and len(min) > 0:
trace[base] = [float(i - j) for i, j in zip(max[0], min)]
atrace = []
for base in list(trace.keys()):
atrace.append(trace[base])
ax = fig.add_subplot(Rows, Cols, num)
pylab.subplots_adjust(wspace=0.5, hspace=0.5)
pylab.title("Region %s" % str(region))
pylab.setp(ax.get_yticklabels(), visible=True)
pylab.setp(ax.get_xticklabels(), visible=False)
for label in ax.get_yticklabels():
label.set_fontsize(8)
pylab.gcf().set_size_inches((Rows + Cols, Rows + Cols))
for t in atrace:
pylab.plot(t)
num += 1
pylab.savefig(self.savepath)
def get_ionograms(top, sffIn, outfolder, key, floworder, metricKey):
nameMap = {'q20Len':'Q20',
'q17Len':'Q17',
'q10Len':'Q10',
'q7Len':'Q7',
'perfect_length':'Perfect'
}
filelist = {}
alignhtml = {}
space_string = {}
for align in top:
alignstring = generate_align_html(align)
row, col = get_row_col(align.get('name'))
fin = Popen("SFFRead %s -C %s -R %s" % (sffIn,col,row), shell=True, stdout=PIPE)
ionogram = fin.stdout.read()
ionogram = ionogram.strip()
ionogram = ionogram.split(" ")
ionogram = [float(i) for i in ionogram]
s = alignstring[1]
expected = []
lenOfIon = len(ionogram)
l = align.get(metricKey)
fskey = template.deseqify(key, floworder)
expected = fskey + list(pylab.zeros(lenOfIon-len(fskey)))
intexp = []
for i in expected:
intexp.append(int(i))
expected = intexp
titleString = 'Single-Well Ionogram for (%s,%s) %s Length=%s Bases' % (int(row), int(col), nameMap.get(metricKey), l)
it = plotters.IonogramJMR(floworder, expected[:len(ionogram)],ionogram,titleString)
it.render()
filelist[align.get('name')] = ("Well_(%s,%s).png" % (int(row),int(col)))
alignhtml[align.get('name')] = alignstring
countLen = math.floor(len(align.get('qDNA.a')))
space_string[align.get('name')] = "".join(get_align_num(countLen))
pylab.savefig(outfolder + "/Well_(%s,%s).png" % (int(row),int(col)))
generateWeb(alignhtml, filelist, outfolder, top, space_string)#space_string, rowCollist)
