bysize_dir = os.path.join(outdir,'by_size/uni_len')
bysize_done = os.path.join(outdir,'by_size.done')
denovo_ref = os.path.join(outdir,'denovo.fa')
if os.path.exists(denovo_ref):
print >> sys.stderr, 'REMOVE REF: %s' % denovo_ref
os.unlink(denovo_ref)
if os.path.exists(bysize_done):
ofbysize = get_uniqued_by_size(bysize_dir)
else:
all_quality = defaultdict(dict)
for uniqued in uniqueds:
load_uniqued(all_quality,uniqued,count_by_ind=True)
print >> sys.stderr, 'LOAD COMPLETE. WRITE BY-SIZE.'
ofbysize = write_uniqued_by_size(all_quality,bysize_dir)
del all_quality
ret = os.system('touch %s' % bysize_done)
sizes = sorted(ofbysize.keys(),reverse=True)
for i in sizes:
print >> sys.stderr, '\nSTART %s' % i
uni = ofbysize[i]
ufq = uniqued_to_fastq(uni)
nreads = get_read_count(ufq)
mm = 0
for c1, c2 in zip(s1, s2):
if c1 != c2:
mm += 1
if mm > dist:
return True
return False
if __name__ == "__main__":
seqlen, dist, uniqueds, outfile = sys.argv[1:]
all_quality = defaultdict(dict)
for u in uniqueds.split(","):
rtd_run.load_uniqued(all_quality, u, count_by_ind=True)
seq_by_len = defaultdict(list)
for k in all_quality.keys():
seq_by_len[len(k)].append(k)
seqs = seq_by_len[int(seqlen)]
seqs.sort()
offby = {}
for i, s in enumerate(seqs):
offby[s] = [si for si in seqs if si != s and not si in offby.keys() and not reject_pair(s, si, int(dist))]
print >>sys.stderr, "\r%s / %s" % (i, len(seqs)),
open(outfile, "w").write(offby.__repr__())
bysize_dir = os.path.join(outdir, 'by_size/uni_len')
bysize_done = os.path.join(outdir, 'by_size.done')
denovo_ref = os.path.join(outdir, 'denovo.fa')
if os.path.exists(denovo_ref):
print >> sys.stderr, 'REMOVE REF: %s' % denovo_ref
os.unlink(denovo_ref)
if os.path.exists(bysize_done):
ofbysize = get_uniqued_by_size(bysize_dir)
else:
all_quality = defaultdict(dict)
for uniqued in uniqueds:
load_uniqued(all_quality, uniqued, count_by_ind=True)
print >> sys.stderr, 'LOAD COMPLETE. WRITE BY-SIZE.'
ofbysize = write_uniqued_by_size(all_quality, bysize_dir)
del all_quality
ret = os.system('touch %s' % bysize_done)
sizes = sorted(ofbysize.keys(), reverse=True)
for i in sizes:
print >> sys.stderr, '\nSTART %s' % i
uni = ofbysize[i]
ufq = uniqued_to_fastq(uni)
nreads = get_read_count(ufq)