def checkMatchedByPrimer(self,activePrimers):
from seqdata import revcomp
from misc import hamming_distance
# go through all active primers in collection
for seq, name in activePrimers:
#print ', '.join([name for seq, name in activePrimers])
# go through all the kmers in the sequence of the handle
for i in range(len(self.sequence)-self.kmerLength):
primer3prime = seq[-self.kmerLength:]
prekmer = self.sequence[i:i+self.kmerLength]
# check if the primer three prime end matches the kmer or the revcomp kmer
for kmer in [prekmer,revcomp(prekmer)]:
if primer3prime == kmer: return name
distance = hamming_distance( primer3prime, kmer )
if distance < self.minHD: return name
if distance < self.minHD+1:
distance = hamming_distance( primer3prime[-5:], kmer[-5:] )
if distance < 1: return name
return False
def checkMatchedByPrimer(self, activePrimers):
from seqdata import revcomp
from misc import hamming_distance
# go through all active primers in collection
for seq, name in activePrimers:
#print ', '.join([name for seq, name in activePrimers])
# go through all the kmers in the sequence of the handle
for i in range(len(self.sequence) - self.kmerLength):
primer3prime = seq[-self.kmerLength:]
prekmer = self.sequence[i:i + self.kmerLength]
# check if the primer three prime end matches the kmer or the revcomp kmer
for kmer in [prekmer, revcomp(prekmer)]:
if primer3prime == kmer: return name
distance = hamming_distance(primer3prime, kmer)
if distance < self.minHD: return name
if distance < self.minHD + 1:
distance = hamming_distance(primer3prime[-5:],
kmer[-5:])
if distance < 1: return name
return False
def check3primEnd(self, kmers, revcompkmers, handles, fiveprime=False):
""" Look at matches between the handle sequence and the kmer collections
"""
from seqdata import revcomp
from misc import hamming_distance
# create dictionary of the kmers in the handle sequence
revcompself = {}
for i in range(len(self.sequence) - self.kmerLength + 1):
if not fiveprime:
kmer = revcomp(self.sequence[i:i + self.kmerLength])
else:
kmer = self.sequence[i:i + self.kmerLength]
try:
revcompself[kmer].append('revcomp self')
except KeyError:
revcompself[kmer] = ['revcomp self']
# check if the active end matches some other kmers in collection
toCLose = False # initial vaule
if fiveprime: # set the sequence we are checking and if we are looking at the three primer or five prime end of the sequence
ENDSEQ = revcomp(self.sequence[:self.kmerLength])
endName = 'first '
else:
ENDSEQ = self.sequence[-self.kmerLength:]
endName = 'last '
assert len(
ENDSEQ
) == self.kmerLength, 'Error: the script is trying to check wrong number of end bases\n'
self.output = '\ngenereated handle#' + str(
self.id) + ' ' + 'check ' + endName + str(
self.kmerLength
) + '=' + ENDSEQ + ':=> ' # give some info for the output
#
# check if 3'/5' of the handle match any sequence in kmers or revcomp-kmers
#
# Look for perfect matches of the end sequence to kmer dictionaries
for dictionary, name in [(revcompself, 'self-rc '), (kmers, ''),
(revcompkmers, 'rc ')]:
if ENDSEQ in dictionary:
self.output += endName + str(
self.kmerLength
) + ' (' + ENDSEQ + ') perfect ' + name + 'match to ' + ' ' + str(
dictionary[ENDSEQ])
self.resonFordeath = name + 'kmer match'
return
# Look for matches with missmatch
for dictionary, name in [(revcompself, 'self-rc'), (kmers, ''),
(revcompkmers, 'rc '),
(revcompself, 'self-rc')]:
for kmer, hits in dictionary.iteritems():
assert len(
kmer
) == self.kmerLength, 'Error: kmer of wrong length: ' + kmer + ' in ' + ', '.join(
hits)
if kmer.count('N'): continue
# check for distance of full kmer to kmer dictionaries
distFull = hamming_distance(ENDSEQ, kmer)
if distFull < self.minHD:
toCLose = True
self.output += str(distFull) + ' mm to ' + str(
hits) + ' (' + kmer + ') too close,'
self.resonFordeath = name + 'kmer match'
break
if distFull < self.minHD + 1: # if almost to close check last five bases so that we have at least 2 nonmatching bases in this part
distLastFive = hamming_distance(ENDSEQ[-5:], kmer[-5:])
if distLastFive < 3:
toCLose = True
self.output += str(
distLastFive) + ' mm in last5 to ' + str(
hits) + ' (' + kmer + ') too close,'
self.resonFordeath = name + 'kmer match in last5 '
break
#if distFull < self.minHD+1 and ENDSEQ[-3] == kmer[-3]: # looks for uniq three mers skip sthis mostly there are non 4**3 is to few
# toCLose = True;
# self.output+= ' lastbase(s) identical, '+name+' '+kmer
# self.resonFordeath = name+'lastbase(s) identical '
# break
#else:output+= str(dist)+' mm to '+str(hits)+' ok '
if toCLose: return
#
# check if 3' bases in handle matches any other 3' in other handles
#
for handle2 in handles:
dist = hamming_distance(ENDSEQ,
handle2.sequence[-self.kmerLength:])
if dist < self.minHD:
toCLose = True
self.output += str(dist) + ' mm to ' + str(
handle2.id) + '(' + handle2.sequence[
-self.kmerLength:] + ')' + ' too close,'
self.resonFordeath = '3 prime ends match'
break
else:
self.output += str(dist) + ' mm to ' + str(
handle2.id) + ' (' + handle2.sequence[
-self.kmerLength:] + ') ' + 'ok |' + ' '
if toCLose: return
def check3primEnd(self, kmers,revcompkmers,handles,fiveprime=False):
""" Look at matches between the handle sequence and the kmer collections
"""
from seqdata import revcomp
from misc import hamming_distance
# create dictionary of the kmers in the handle sequence
revcompself = {}
for i in range(len(self.sequence)-self.kmerLength+1):
if not fiveprime: kmer = revcomp(self.sequence[i:i+self.kmerLength])
else: kmer = self.sequence[i:i+self.kmerLength]
try: revcompself[kmer].append('revcomp self')
except KeyError:revcompself[kmer] = ['revcomp self']
# check if the active end matches some other kmers in collection
toCLose = False # initial vaule
if fiveprime: # set the sequence we are checking and if we are looking at the three primer or five prime end of the sequence
ENDSEQ = revcomp(self.sequence[:self.kmerLength])
endName = 'first '
else:
ENDSEQ = self.sequence[-self.kmerLength:]
endName = 'last '
assert len(ENDSEQ) == self.kmerLength, 'Error: the script is trying to check wrong number of end bases\n'
self.output = '\ngenereated handle#'+str(self.id)+' '+'check '+endName+str(self.kmerLength)+'='+ENDSEQ+':=> ' # give some info for the output
#
# check if 3'/5' of the handle match any sequence in kmers or revcomp-kmers
#
# Look for perfect matches of the end sequence to kmer dictionaries
for dictionary, name in [(revcompself,'self-rc '),(kmers,''),(revcompkmers,'rc ')]:
if ENDSEQ in dictionary:
self.output+= endName+str(self.kmerLength)+' ('+ENDSEQ+') perfect '+name+'match to '+' '+str(dictionary[ENDSEQ]);
self.resonFordeath = name+'kmer match'
return
# Look for matches with missmatch
for dictionary, name in [(revcompself,'self-rc'),(kmers,''),(revcompkmers,'rc '),(revcompself,'self-rc')]:
for kmer,hits in dictionary.iteritems():
assert len(kmer) == self.kmerLength, 'Error: kmer of wrong length: '+kmer+' in '+', '.join(hits)
if kmer.count('N'): continue
# check for distance of full kmer to kmer dictionaries
distFull = hamming_distance(ENDSEQ,kmer)
if distFull < self.minHD:
toCLose = True;
self.output+= str(distFull)+' mm to '+str(hits)+' ('+kmer+') too close,'
self.resonFordeath = name+'kmer match'
break
if distFull < self.minHD+1: # if almost to close check last five bases so that we have at least 2 nonmatching bases in this part
distLastFive = hamming_distance(ENDSEQ[-5:],kmer[-5:])
if distLastFive < 3:
toCLose = True;
self.output+= str(distLastFive)+' mm in last5 to '+str(hits)+' ('+kmer+') too close,'
self.resonFordeath = name+'kmer match in last5 '
break
#if distFull < self.minHD+1 and ENDSEQ[-3] == kmer[-3]: # looks for uniq three mers skip sthis mostly there are non 4**3 is to few
# toCLose = True;
# self.output+= ' lastbase(s) identical, '+name+' '+kmer
# self.resonFordeath = name+'lastbase(s) identical '
# break
#else:output+= str(dist)+' mm to '+str(hits)+' ok '
if toCLose: return
#
# check if 3' bases in handle matches any other 3' in other handles
#
for handle2 in handles:
dist = hamming_distance(ENDSEQ,handle2.sequence[-self.kmerLength:])
if dist < self.minHD:
toCLose = True;
self.output+= str(dist)+' mm to '+str(handle2.id)+'('+handle2.sequence[-self.kmerLength:]+')'+' too close,'
self.resonFordeath = '3 prime ends match'
break
else: self.output+= str(dist)+' mm to '+str(handle2.id)+' ('+handle2.sequence[-self.kmerLength:]+') '+'ok |'+' '
if toCLose: return