def amplitude_from_abif(filename):
''' f
Return amplitude dictionnary for each base.
filename : sanger data abif format
seq : compute amplitude only for a sub sequence
'''
abif = Trace(filename)
ampl = abif.get_data("P1AM1")
output = []
index = 0
end = len(abif.seq)
while index < end :
base = abif.seq[index]
output.append((base,abif.get_data("P1AM1")[index]))
index+=1
return output
def amplitude_from_abif(filename):
''' f
Return amplitude dictionnary for each base.
filename : sanger data abif format
seq : compute amplitude only for a sub sequence
'''
abif = Trace(filename)
ampl = abif.get_data("P1AM1")
output = []
index = 0
end = len(abif.seq)
while index < end:
base = abif.seq[index]
output.append((base, abif.get_data("P1AM1")[index]))
index += 1
return output
def __init__(self,filename,ratio,q_set):
traceObject = Trace(filename)
self.ratio = float(ratio)
self.q_set = int(q_set)
self.primarySeq = []
self.secondarySeq = []
self.trim5 = 0
self.trim3 = 0
self.order = list( traceObject.get_data('FWO_1') ) # The Order of the lightwave of Nucleotides
self.primary_basecalls = traceObject.get_data('PBAS2') # Bases called by the basecaller of machine
self.primary_quality = traceObject.get_data('PCON2') # Base Quality by basecaller
self.primary_basecallPos = np.array( traceObject.get_data('PLOC2')) # Primary Peak Location called by the basecaller
'''Unprocessed RAW DATA'''
### Analyzed Color Data
self.traceMatrix = np.array( [ traceObject.get_data('DATA9'),
traceObject.get_data('DATA10'),
traceObject.get_data('DATA11'),
traceObject.get_data('DATA12') ])
#self.peakPosMatrix , self.peakAmpMatrix = self.getPeakPosAndAmp()
correction = True
try:
self.primary_peakAmp = np.array( traceObject.get_data('P1AM1')) # Primary Peak Amp called by the basecaller
self.secondary_peakAmp = np.array( traceObject.get_data('P2AM1'))
self.secondary_peakBase = traceObject.get_data('P2BA1')
except KeyError:
correction = False
self.background_value = None;
self.primarySeq , self.secondarySeq , self.trim5 , self.trim3 = self.makebasecall(self.ratio,self.q_set,correction)
def main(trace, seq, gene2locus):
'''
tracefile, seq, make sure trace and seq correspend to each other correctly
return heterosite{}
'''
heteroSite = {}
gft2base = {}
st = Trace(trace)
startBase = SKIP_BASE_NUM
endBase = len(st.seq) - SKIP_BASE_NUM
st.basepos = st.get_data('PLOC1')
st.basecalls = st.seq
st.tracesamps = {'G': (), 'A': (), 'T': (), 'C': ()}
st.tracesamps['G'], st.tracesamps['A'], st.tracesamps['T'], st.tracesamps[
'C'] = st.get_data('DATA9'), st.get_data('DATA10'), st.get_data(
'DATA11'), st.get_data('DATA12')
#detect hetero base
i = 0
for basePos in st.basepos[startBase:endBase]:
#base posGATC
i += 1
tracePos = [
st.tracesamps['G'][basePos], st.tracesamps['A'][basePos],
st.tracesamps['T'][basePos], st.tracesamps['C'][basePos]
]
if max(tracePos) < TRACE_THRESHOLD:
continue
stdMn = calSimilty(
sorted(tracePos, reverse=True)[:2]
) #calculate the first two largest trace value's similarity by formula: std / mean
if stdMn > SIMILTY_THRESHOLD:
continue
altBase = baseOrderDict[getSecondLarge(tracePos)]
heteroPos = startBase + i
if heteroPos not in heteroSite:
heteroSite[heteroPos] = [st.basecalls[startBase + i - 1], altBase]
else:
pass
if args.debug.lower() == 'y':
print(
'{orgbasePos}\t{pos}\t{base}\t{G}\t{A}\t{T}\t{C}\t{stdMn}\t{altBase}'
.format(base=st.basecalls[startBase + i - 1],
G=st.tracesamps['G'][basePos],
A=st.tracesamps['A'][basePos],
T=st.tracesamps['T'][basePos],
C=st.tracesamps['C'][basePos],
stdMn=stdMn,
pos=startBase + i,
orgbasePos=basePos,
altBase=altBase))
#run blastn
cmd = 'blastn -query "{0}" -db {1} -evalue 0.01 -outfmt "6 qseqid sseqid qstart qend sstart send qseq sseq btop" -num_threads 8 -task megablast -max_target_seqs 1'.format(
seq, refSeq)
logging.debug(cmd)
blastRes = os.popen(cmd).read()
#extract base content
qseqid, sseqid, qstart, qend, sstart, send, qseq, sseq, btop = blastRes.rstrip(
).split('\t')
assert sseqid in gene2locus, '{0} not valid gene id'.format(sseqid)
for gftid, cord in gene2locus[sseqid].items():
if (int(sstart) <= int(cord) <= int(send)):
#hit within range
pos = int(qstart) + int(cord) - int(sstart)
if pos in heteroSite: #encounter a hetero site
gft2base[gftid] = ''.join(heteroSite[pos])
else:
gft2base[gftid] = '{0}{0}'.format(qseq[int(cord) -
int(sstart) - 1])
else:
#hit W/O range
pass
return gft2base
