How to use bitarray - 10 common examples
To help you get started, we’ve selected a few bitarray examples, based on popular ways it is used in public projects.
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bvernot / freezing-archer / bin / myBedTools3.py View on Github 
code.fromfile(file, 8)
if code.to01() != myBedTools.binaryseqfilegenome_code:
print "unexpected code for binary seq file genome!"
print "code: ", code
print "expected: ", myBedTools.binaryseqfilegenome_code
sys.exit(-1)
try:
chr_byte_start = self.chr_offset[exp_chr] * self.factor // 8
chr_partial_byte_start = (self.chr_offset[exp_chr] * self.factor) % 8
print 'starting at', chr_byte_start, 'bytes, with', chr_partial_byte_start, 'offset'
file.seek(chr_byte_start, 0)
ar.fromfile(file, self.chr_lens[exp_chr] * self.factor + 16)
print ar[0:100]
except EOFError:
pass
if ar.length() != bitarray_m.bits2bytes(self.chr_lens[exp_chr] * self.factor) * 8:
print "expected length of array to match given start and end!"
print filename
print ar.length(), bitarray_m.bits2bytes(self.genome_len * self.factor), self.genome_len * self.factor
sys.exit(-1)
pass
# shorten ar to genome_len
for i in xrange(ar.length() - self.genome_len * self.factor):
#print self.genome_len, ar.length(), 'popping'
ar.pop()
pass
self.bases = ar
pass
elif self.output_type == myBedTools.binaryseqfilegenome:
infile = myBedTools.open_file(filename, discard_header = header)See: https://github.com/JohannesBuchner/imagehash/blob/4.0/imagehash/__init__.py#L125
"""
parser = PIL.ImageFile.Parser()
parser.feed(image_data)
img = parser.close()
target_size = (__class__.IMG_SIG_SIZE, __class__.IMG_SIG_SIZE)
img.thumbnail(target_size, PIL.Image.BICUBIC)
if img.size != target_size:
logging.getLogger("Cover").debug("Non square thumbnail after resize to %ux%u, unable to compute signature" % target_size)
return None
img = img.convert(mode="RGB")
pixels = img.getdata()
pixel_count = target_size[0] * target_size[1]
color_count = 3
r = bitarray.bitarray(pixel_count * color_count)
r.setall(False)
for ic in range(color_count):
mean = sum(p[ic] for p in pixels) // pixel_count
for ip, p in enumerate(pixels):
if p[ic] > mean:
r[pixel_count * ic + ip] = True
return r
def generate_bitarray(self, length):
return bitarray(
''.join('1' if random.random() > 0.5 else '0' for _ in range(length))
)def gen_bits(N):
#
if N < 1:
return None
if N == 1:
b = BitBuffer()
b.set_bit(0)
yield b
b = BitBuffer()
b._wpos = 0
b.set_bit(1)
yield b
else:
p = (1<def gen_bits(N):
#
if N < 1:
return None
if N == 1:
b = BitBuffer()
b.set_bit(0)
yield b
b = BitBuffer()
b._wpos = 0
b.set_bit(1)
yield b
else:
p = (1<b = BitBuffer()
b.set_bit(0)
yield b
b = BitBuffer()
b._wpos = 0
b.set_bit(1)
yield b
else:
p = (1<def gen_bits(N):
#
if N < 1:
return None
if N == 1:
b = BitBuffer()
b.set_bit(0)
yield b
b = BitBuffer()
b._wpos = 0
b.set_bit(1)
yield b
else:
p = (1<pass
code.fromfile(file, 8)
if code.to01() != myBedTools.binaryseqfilegenome_code:
print "unexpected code for binary seq file genome!"
print "code: ", code
print "expected: ", myBedTools.binaryseqfilegenome_code
sys.exit(-1)
try:
#ar.fromfile(file, self.genome_len * self.factor + 16)
ar.fromfile(file)
except EOFError:
pass
if ar.length() != bitarray_m.bits2bytes(self.genome_len * self.factor) * 8:
print "expected length of array to match given start and end!"
print filename
print ar.length(), bitarray_m.bits2bytes(self.genome_len * self.factor), self.genome_len * self.factor
sys.exit(-1)
pass
# shorten ar to genome_len
for i in xrange(ar.length() - self.genome_len * self.factor):
#print self.genome_len, ar.length(), 'popping'
ar.pop()
pass
self.bases = ar
pass
elif filetype == self.binaryseqfilegenomechr:
print "THIS DOESN'T WORK"
sys.exit(-1)
ar = bitarray()
code = bitarray()file = gzip.open(filename, 'r')
else:
file = open(filename, 'r')
pass
code.fromfile(file, 8)
if code.to01() != myBedTools.binaryseqfilegenome_code:
print "unexpected code for binary seq file genome!"
print "code: ", code
print "expected: ", myBedTools.binaryseqfilegenome_code
sys.exit(-1)
try:
#ar.fromfile(file, self.genome_len * self.factor + 16)
ar.fromfile(file)
except EOFError:
pass
if ar.length() != bitarray_m.bits2bytes(self.genome_len * self.factor) * 8:
print "expected length of array to match given start and end!"
print filename
print ar.length(), bitarray_m.bits2bytes(self.genome_len * self.factor), self.genome_len * self.factor
sys.exit(-1)
pass
# shorten ar to genome_len
for i in xrange(ar.length() - self.genome_len * self.factor):
#print self.genome_len, ar.length(), 'popping'
ar.pop()
pass
self.bases = ar
pass
elif filetype == self.binaryseqfilegenomechr:
print "THIS DOESN'T WORK"ar = bitarray()
code = bitarray()
file = open(filename, 'r')
#code.fromfile(file)
code.fromfile(file, 8)
if code.to01() != myBedTools.binarybedfilegenome_code:
print "unexpected code for binary bed file genome!"
print "code: ", code
print "expected: ", myBedTools.binarybedfilegenome_code
sys.exit(-1)
try:
#ar.fromfile(file, self.genome_len + 16)
ar.fromfile(file)
except EOFError:
pass
if ar.length() != bitarray_m.bits2bytes(self.genome_len) * 8:
print "expected length of array to match given start and end!"
print filename
print ar.length(), bitarray_m.bits2bytes(self.genome_len), self.genome_len
sys.exit(-1)
pass
# shorten ar to genome_len
for i in xrange(ar.length() - self.genome_len):
#print self.genome_len, ar.length(), 'popping'
ar.pop()
pass
#### COULD CHECK FNS FOR BITARRAY STUFF (AND, OR ETC)
if not self.initialize:
self.initialize = True
if fn == myBedTools.set_to_one:
self.bases = ar
elif fn == myBedTools.set_to_zero:bitarray
efficient arrays of booleans -- C extension
