foo= ""

for i in range(len(string)):

foo+=string[:i] + '.' + string[i+1:] + "|"

rcd = ""

rcs = {"A":"T","C":"G","T":"A","G":"C", "N":"N"}

for char in seq[::-1]:

rcd+=rcs[char]

for bc in barcodes:

match = False

hd = hamming(barcode, bc)

if hd <= 2:

match = True

barcode = bc

break

'''Takes a Fastq filehandle in and filehandle out for each read; writes barcode-clipped fastqs to\

filehandle out and returns a dictionary with barcode pairs associated with given read names'''

seq_r1 = FastqGeneralIterator(fhi_r1)

seq_r2 = FastqGeneralIterator(fhi_r2)

seqzip = it.izip(seq_r1, seq_r2) #zip up the two fastq iterators to increase performance

bc_seq = {}

bc1s = [] #Container to store internal barcode IDs

bridge = ''

#Create a list of all possible internal barcodes (necessary

#for hamming distance calculations)

for line in internal_bc:

bc = line.rstrip('\n')

strip = 'GATC' + bc + 'GAATTC'

bc1s.append(bc)

bridge_re = re.compile('GATC[ACGT]{8}GAATTC')

#We want to find all reads where

#the internal adaptor is present

#in either R1 or R2. Accepting that we're

#throwing out some stuff because of mismatches,

##let's just use the re module to do this.

for i in seqzip:

title1, seq1, qual1 = i[0]

title2, seq2, qual2 = i[1]

new_title = title1.split()[0]

m1 = bridge_re.search(seq1)

m2 = bridge_re.search(seq2)

terminal_bc = title1.split('&')[1]

if m1:

if m2:

pos1 = m1.start()

pos2 = m2.start()

trim_seq1 = seq1[:pos1]

trim_seq2 = seq2[:pos2]

trim_qual1 = qual1[:pos1]

trim_qual2 = qual2[:pos2]

#Check for length of the read

if len(trim_seq1) < 30 or len(trim_seq2) < 30:

continue #and continue if either one is too short

barcode_seq1 = seq1[pos1 + 4:pos1 + 12]

barcode_seq2 = seq2[pos2 + 4:pos2 + 12]

ham_bc1 = checkHamming(bc1s, barcode_seq1)

ham_bc2 = checkHamming(bc1s, barcode_seq2)

if ham_bc1[0]:

if ham_bc2[0]:

print >> fho_r1, "@%s\n%s\n+\n%s" % (new_title, trim_seq1, trim_qual1)

print >> fho_r2, "@%s\n%s\n+\n%s" % (new_title, trim_seq2, trim_qual2)

bc1 = ham_bc1[1]

bc2 = ham_bc2[1]

print "%s\t%s\t%s\t%s" % (new_title, bc1, bc2, terminal_bc)

else:

pos1 = m1.start()

pos1_end = m1.end()

trim_seq1 = seq1[:pos1]

trim_qual1 = qual1[:pos1]

#Check for length of the rea

if len(trim_seq1) < 30:

continue #and continue if either one is too short

if len(seq1[pos1_end:]) < 12:

continue

barcode_seq2 = rc(seq1[pos1_end:pos1_end + 8])

barcode_seq1 = seq1[pos1 + 4:pos1 + 12]

ham_bc1 = checkHamming(bc1s, barcode_seq1)

ham_bc2 = checkHamming(bc1s, barcode_seq2)

if ham_bc1[0]:

if ham_bc2[0]:

print >> fho_r1, "@%s\n%s\n+\n%s" % (new_title, trim_seq1, trim_qual1)

print >> fho_r2, "@%s\n%s\n+\n%s" % (new_title, seq2, qual2)

bc1 = ham_bc1[1]

bc2 = ham_bc2[1]

print "%s\t%s\t%s\t%s" % (new_title, bc1, bc2, terminal_bc)

else:

if m2:

pos2 = m2.start()

pos2_end = m2.end()

trim_seq2 = seq2[:pos2]

trim_qual2 = qual2[:pos2]

#Check for length of the read

# print seq2[pos2_end:]

if len(trim_seq2) < 30:

continue #and continue if either one is too short

if len(seq2[pos2_end:]) < 12:

continue #and continue if either one is too short

barcode_seq1 = rc(seq2[pos2_end:pos2_end + 8])

barcode_seq2 = seq2[pos2 + 4:pos2 + 12]

ham_bc1 = checkHamming(bc1s, barcode_seq1)

ham_bc2 = checkHamming(bc1s, barcode_seq2)

if ham_bc1[0]:

if ham_bc2[0]:

print >> fho_r1, "@%s\n%s\n+\n%s" % (new_title, seq1, qual1)

print >> fho_r2, "@%s\n%s\n+\n%s" % (new_title, trim_seq2, trim_qual2)

bc1 = ham_bc1[1]

bc2 = ham_bc2[1]

fhi_bc = open(sys.argv[1])

fhi_r1 = open(sys.argv[2])

fhi_r2 = open(sys.argv[3])

fho_r1 = open(sys.argv[4], 'w')

fho_r2 = open(sys.argv[5], 'w')

assoc = associateBarcodes(fhi_r1, fhi_r2, fho_r1, fho_r2, fhi_bc)

fhi_bc.close()

fhi_r1.close()

fhi_r2.close()

fho_r1.close()