def generate_align_html(alignment):
ret = []
inter = []
for i in alignment.get('qDNA.a'):
inter.append(colorify(i.upper()))
ret.append(inter)
inter = []
for i in alignment.get('match.a'):
inter.append(colorify(i.upper()))
ret.append(inter)
inter = []
for i in alignment.get('tDNA.a'):
inter.append(i.upper())
ret.append(inter)
return ret
def gen_colorify(rowCol, alignstringfill):
align = []
inter = []
index = 0
for i in alignstringfill[rowCol][:3]:
if index != 2:
inter.append(colorify(i.upper()))
index += 1
else:
inter.append(i.upper())
return inter
def ionograms(metrics):
"""generage ionograms from tf information"""
for k, v in metrics.iteritems():
title = str(k)
savePaths = []
alignment = []
for i in range(10):
key = "Top " + str(i + 1)
if key in v:
index = i + 1
e = v[key]
splitE = e.split(",")
row = splitE[0]
col = splitE[1]
pre = splitE[2]
post = splitE[3]
ideal = splitE[4]
bars = splitE[5]
called = splitE[6]
preA = [float(i) for i in pre.strip().split(" ")]
postA = [float(i) for i in post.strip().split(" ")]
rowCol = "(%s,%s)" % (row, col)
header = title + " Pre-Corrected " + rowCol
preIonogram = plotters.IonogramJMR("TACG", preA[: len(preA)], preA[: len(preA)], header)
preIonogram.render()
preSavePath = "Pre-Corrected_%s_%s.png" % (index, title)
pylab.savefig(preSavePath)
header = title + " Post-Corrected " + rowCol
preIonogram = plotters.IonogramJMR("TACG", postA[: len(postA)], postA[: len(postA)], header)
preIonogram.render()
postSavePath = "Post-Corrected_%s_%s.png" % (index, title)
pylab.savefig(postSavePath)
savePaths.append([preSavePath, postSavePath])
alignment = [called, bars, ideal]
alignhtml = []
index = 0
for string in alignment:
ainter = []
if index != 2:
index += 1
for i in string:
ainter.append(colorify(i.upper()))
else:
for i in string:
ainter.append(i.upper())
alignhtml.append(ainter)
# print savePaths
if len(savePaths) > 0:
generateWeb(savePaths, title, alignhtml)
def blastToIonogram(blastPath, displayNum, byLength, key, floworder, getPerfect):
blast = open(blastPath, "r")
fullRowCol = {}
firstIdentity = []
alignstring = {}
startVal = {}
endVal = {}
currentQuery = None
for line in blast:
if "Iteration_query-def>" in line:
if line not in fullRowCol:
line = line.strip()
line = line.strip().split(">")
line = line[1].split("<")
line = str(line[0])
line = line.strip()
fullRowCol[line] = []
alignstring[line] = []
currentQuery = line
if byLength:
if "Hsp_qseq" in line:
fullRowCol[currentQuery].append(line.strip())
else:
if "Hsp_bit-score" in line:
fullRowCol[currentQuery].append(line.strip())
if "Hsp_query-from" in line:
alignstring[currentQuery].append(line.strip())
if "Hsp_query-to" in line:
alignstring[currentQuery].append(line.strip())
if "Hsp_align-len" in line:
alignstring[currentQuery].append(line.strip())
if "Hsp_positive" in line:
alignstring[currentQuery].append(line.strip())
if "Hsp_qseq" in line:
alignstring[currentQuery].append(line.strip())
if "Hsp_midline" in line:
alignstring[currentQuery].append(line.strip())
if "Hsp_hseq" in line:
alignstring[currentQuery].append(line.strip())
#print alignstring
alignstringfill = {}
for k,v in alignstring.iteritems():
curval = None
curkey = None
bars = None
if len(v)>0:
fr = v[0].split(">")
fr = fr[1].split("<")
fr = fr[0]
#print fr
to = v[1].split(">")
to = to[1].split("<")
to = to[0]
#print to
pos = v[2].split(">")
pos = pos[1].split("<")
pos = pos[0]
#print pos
lengt = v[3].split(">")
lengt = lengt[1].split("<")
lengt = lengt[0]
#print length
q = v[4].split(">")
q = q[1].split("<")
q=q[0]
#print q
s = v[5].split(">")
s = s[1].split("<")
s = s[0]
#print s
bars = v[6].split(">")
bars = bars[1].split("<")
bars = bars[0]
#print bars
output = [q,bars,s,fr,to,pos,lengt]
curKey = k.split("|")
row = curKey[0].split("r")[-1]
col = curKey[1].split("c")[-1]
rowcol = (int(row), int(col))
alignstringfill[rowcol] = output
#print fullRowCol
filtered = {}
for k,v in fullRowCol.iteritems():
curVal = None
curKey = None
if len(v) > 0:
curVal = v[0].split(">")
curVal = curVal[1].split("<")
curVal = curVal[0]
curKey = k.split("|")
row = curKey[0].split("r")[-1]
col = curKey[1].split("c")[-1]
rowcol = (int(row), int(col))
if byLength:
filtered[rowcol] = length(curVal)
else:
filtered[rowcol] = float(curVal)
sortedWells = sorted(filtered.items(), key=itemgetter(1), reverse = True)
topfive = []
classData = []
readsVcycles = []
perfect_alignments = []
for rowcol,val in sortedWells:
dif = abs(int(alignstringfill[rowcol][3])-int(alignstringfill[rowcol][4]))
to = int(alignstringfill[rowcol][4])
fro = int(alignstringfill[rowcol][3])
string = alignstringfill[rowcol][0]
matched = alignstringfill[rowcol][5]
lengt = alignstringfill[rowcol][6]
if 'N' not in string:
if to<3 or fro<3 and dif>21:
topfive.append((rowcol,val))
classData.append((rowcol,val,dif,string))
if matched == lengt:
perfect_alignments.append((rowcol,val))
if getPerfect:
topfive = perfect_alignments[:displayNum]
else:
topfive = topfive[:displayNum]
if len(classData)<10000:
cycles_vs_align_len(classData, blastPath, floworder)
else:
cycles_vs_align_len(classData[:10000], blastPath, floworder)
alignmenthtml = {}
space_string = {}
for rowcol,val in topfive:
inter = []
index = 0
for i in alignstringfill[rowcol][:3]:
if index == 0:
inter.append(i.upper())
index += 1
else:
inter.append(colorify(i.upper()))
alignmenthtml[rowcol] = inter
countLen = math.floor(len(alignstringfill[rowcol][:3][0]))
#print alignstringfill[rowcol][:3][0]
space_string[rowcol] = "".join(get_align_num(countLen))
return (topfive, alignmenthtml, alignstringfill, space_string)
from colorify import *
# initializing COLORIFY
init_colorify()
#this will generate text in random color
for i in range(10):
print(colorify("Random Colored text"))
# text color = green
print(colorify("Sucess", C.green))
# text color = black , background color = green
print(colorify("Sucess", C.black, C.green))
print(colorify("Error ", C.red))
print(colorify("Error ", C.white, C.red))
print(colorify("Alert ", C.orange))
print(colorify("Alert ", C.black, C.orange))
print(colorify("Info ", C.blue))
print(colorify("Info ", C.white, C.crimson))
#this will print all the color
printAllColor()
