def close_enough_old(self, primer, sequence, errors) :
err_count = 0
for i,j in zip(sequence, primer) :
if not IUPAC.equal(i, j) :
err_count += 1
#if len(a) > 10 :
# print a, b, err_count
return err_count <= errors
def close_enough(self, primer, sequence, diff) :
if diff < 0 :
return False
if (len(primer) == 0) or (len(sequence) == 0) :
return True
m = IUPAC.equal(sequence[0], primer[0])
return self.close_enough(primer[1:], sequence[1:], diff if m else diff-1) or \
self.close_enough(primer[1:], sequence, diff-1) or \
self.close_enough(primer, sequence[1:], diff-1)
def accept(self, seq) :
seqprimer = seq.sequence[:self.len]
ret = IUPAC.close_enough(self.primer, seq.sequence, self.err)
#print self.primer, seq.sequence[:self.len], ret
if ret and self.clip :
# primer part of sequence may be longer or
# shorter, but it does not really matter
# as terminal gaps are not included in our
# definition of identity
seq.remove_mid(self.len)
return ret
def read_nematodes(self, fastq_fname, fprimer, rprimer, diffs, length) :
tmp = []
acc2name = {}
# read in sequences
fq = FastqFile(fastq_fname)
fq.open()
for seq in fq :
if 'Nematoda' not in seq.id :
continue
seq.ungap()
seq.back_translate()
new_id = seq.id.split()[0][1:]
tmp.append((new_id, seq.sequence))
acc2name[new_id] = seq.id[seq.id.find('Nematoda'):]
fq.close()
# test sequences
p = Progress("Looking for primer sequences", len(tmp), False)
p.start()
tmp2 = []
for label,seq in tmp :
findex = IUPAC.seq_position(fprimer, seq, diffs)
if findex != -1 :
#if IUPAC.seq_position_reverse(rprimer, seq, diffs) != -1 :
shortseq = seq[findex + len(fprimer) : findex + len(fprimer) + length]
if 'N' not in shortseq :
tmp2.append((label, shortseq))
p.increment()
p.end()
return tmp2,acc2name
def distance(self, aligned) :
leng = float(min(len(aligned[0]), len(aligned[1])))
last_gap = True
diff = 0
for c1,c2 in zip(aligned[0], aligned[1]) :
if (c1 == '-') and (c2 == '-') :
continue
gap = '-' in (c1,c2)
if last_gap and gap :
continue
if not IUPAC.equal(c1, c2) :
diff += 1
last_gap = gap
if last_gap :
diff -= 1
return (leng - diff) / leng
def extract(self, sff, outdir, primer, primer_errors, barcode, barcode_errors, max_homopolymer) :
try :
from Bio import SeqIO
except ImportError :
print >> sys.stderr, "BioPython not installed (only required for working with SFF files)"
sys.exit(1)
barcode_len = len(barcode)
primer_len = len(primer)
raw_seq_total = 0
names = []
flows = []
flowlens = []
for record in SeqIO.parse(sff.get_filename(), "sff") :
raw_seq_total += 1
good_bases = record.seq[record.annotations["clip_qual_left"] : record.annotations["clip_qual_right"]]
barcode_seq = good_bases[:barcode_len]
primer_seq = good_bases[barcode_len : barcode_len + primer_len]
new_length = 0
for i in range(0, len(record.annotations["flow_values"]), 4) :
signal = 0
noise = 0
for j in range(4) :
f = float(record.annotations["flow_values"][i + j]) / 100.0
if int(f + 0.5) > max_homopolymer :
break
if f > 0.5 :
signal += 1
if f < 0.7 :
noise += 1
if noise > 0 or signal == 0 :
break
new_length += 1
new_length *= 4
if new_length > 450 :
new_length = 450
if new_length >= 360 and \
IUPAC.close_enough(barcode, barcode_seq, barcode_errors) and \
IUPAC.close_enough(primer, primer_seq, primer_errors) :
flows.append(record.annotations["flow_values"])
flowlens.append(new_length)
names.append(record.id)
if len(flows) == 0 :
self.log.info("kept 0/%d sequences" % raw_seq_total)
return 0, None
# output pyronoise input file
# see http://userweb.eng.gla.ac.uk/christopher.quince/Software/PyroNoise.html
f = open(join(outdir, "flows.dat"), 'w')
print >> f, "%d %d" % (len(flows), max([ len(i) for i in flows ]))
for i in range(len(flows)) :
print >> f, " ".join([ names[i], str(flowlens[i]) ] + [ "%.2f" % (float(i) / 100.0) for i in flows[i] ])
f.close()
self.log.info("kept %d/%d sequences" % (len(flows), raw_seq_total))
return len(flows), f.name
