def count_unmapped(sam_file): ''' Print number of unmapped reads in sam_file. ''' mapped = 0 unmapped = 0 for data in sc_read_simple_tab_file(sam_file): read_id = data[0] match = data[2] if match == "*": unmapped += 1 else: mapped += 1 print unmapped, mapped, "\r", print print "Unmapped %s from %s mapped" % (unmapped, mapped) return (mapped, unmapped)
def check_adapters(settings):
'''
'''
print "Load library for key=", settings["k"]
with open(settings["pickle_libraries_file"]) as fh:
library = cPickle.load(fh)
library = library[settings["k"]]
assert len(library.keys()[0]) == settings["k"]
print "Library size:", len(library.keys())
contaminated_kmers = {}
print "Iter over kmers"
for i, d in enumerate(sc_read_simple_tab_file(settings["fastq_file"])):
(kmer, tf) = d
tf = int(tf)
kmer = kmer.lower()
print i, kmer, tf, "\r",
if settings["cutoff"] and tf < settings["cutoff"]:
break
rkmer = get_revcomp(kmer)
if kmer in library or rkmer in library:
print
print kmer, tf, library[kmer]
contaminated_kmers[kmer] = (tf, library[kmer])
all_kmers = set(contaminated_kmers.keys())
contaminated_kmers = contaminated_kmers.items()
contaminated_kmers.sort(key=lambda x: x[1], reverse=True)
print "Save data"
with open(settings["output_file"], "w") as fh:
for (k, v) in contaminated_kmers:
rkey = get_revcomp(k)
s = "%s\t%s\n" % (k, v)
fh.write(s)
if not rkey in all_kmers:
s = "%s\t%s\n" % (rkey, v)
fh.write(s)
return contaminated_kmers
