def query_library_bytes_shm(genome, sequence, shm_genome_bytes):
library_bytes = shm_genome_bytes
query_bytes = np.array([ bytes_translation_dict.get(sequence[(j)*4:(j)*4+4],0)
for j in range(5)],
dtype=np.dtype("uint8"))
mismatches_threshold = 5
f = library_bytes
g = query_bytes
h = np.zeros((len(library_bytes)/len(query_bytes),), dtype = np.dtype("uint32"))
import bc
n_matches = bc.striding_8bit_comparison(f,g,h,mismatches_threshold)
matches_list = h[:n_matches]
print "GENOME: {0}".format(genome)
print "N MATCHES: ", len(matches_list)
#return matches_list[:100]
return matches_list
def query_library_bytes(nlines):
print "starting query, loading lib"
LIBRARY_BYTES_PATH = os.path.join(RD_DATAROOT,"{0}_bytes.npy".format(nlines))
with open(LIBRARY_BYTES_PATH) as f:
library_bytes = np.load(f)
print "loaded lib, setting up query bytes"
tests = []
for e in re.compile(">", re.M).split(ltests.strip()):
if not e: continue
match = re.compile( "(?P<id>.*)\n(?P<guide>\S{20})\s*(?P<nrg>\S{3})",re.M).search(e)
tests.append(match.groupdict())
query_bytes = np.array([bytes_translation_dict[tests[0]["guide"][(j)*4:(j)*4+4]]
for j in range(5)],
dtype=np.dtype("uint8"))
threshold_mismatches = 4
bits_mismatch_threshold = threshold_mismatches
f = library_bytes
g = query_bytes
h = np.zeros((len(library_bytes)/len(query_bytes),), dtype = np.dtype("uint32"))
print "running comparison"
import bc
times = [utcnow()]
n_matches = bc.striding_8bit_comparison(f,g,h,bits_mismatch_threshold)
times+=[utcnow()]
compare_time = times[1] - times[0]
print "compared {0} matches in {1} ({2} microsec/ million)".format(len(library_bytes), compare_time,(compare_time.seconds * 1e6 + compare_time.microseconds)/(float(len(library_bytes)/1e6)) )
matches_list = h[:n_matches]
print "done comparing, computing NZ elts"
#matches = np.nonzero(h)[0]
print "python, n_matches: {0}".format(n_matches)
print "first match: {0}".format(matches_list[0])
def query_library_bytes_shm(genome, sequence, shm_genome_bytes):
library_bytes = shm_genome_bytes
query_bytes = np.array([
bytes_translation_dict.get(sequence[(j) * 4:(j) * 4 + 4], 0)
for j in range(5)
],
dtype=np.dtype("uint8"))
mismatches_threshold = 5
f = library_bytes
g = query_bytes
h = np.zeros((len(library_bytes) / len(query_bytes), ),
dtype=np.dtype("uint32"))
import bc
n_matches = bc.striding_8bit_comparison(f, g, h, mismatches_threshold)
matches_list = h[:n_matches]
print "GENOME: {0}".format(genome)
print "N MATCHES: ", len(matches_list)
#return matches_list[:100]
return matches_list
