def rip_pages(self, start, end, filepath):
last = end + 1
pages = last - start
f = open(filepath, 'a+')
# Add S0 header record
f.write(SRecord(STYPES['S0'], bytearray([0x00, 0x00]), binascii.hexlify("S19 ripped by fuct")).print_srec() + '\r\n')
for i, page in enumerate(xrange(start, last)):
addr = 0x8000
rec_len = 16
progress = float(i) / pages
common.print_progress(progress)
self.__set_page(page)
page_data = binascii.hexlify(self.__read_page()).upper()
# Trim empty flash from start and end of pages
first_index = len(page_data)
for index in xrange(0, len(page_data), 2):
if page_data[index:index + 2] != 'FF':
first_index = index
break
first_index = (first_index // rec_len) * rec_len
last_index = 0
for index in xrange(len(page_data), 0, -2):
if page_data[index - 2:index] != 'FF':
last_index = index
break
page_data = page_data[first_index:last_index]
addr += first_index // 2
# Split data into lines of readable length and stringify
records = ''
while len(page_data):
rec_data = page_data[:rec_len * 2]
records += SRecord(STYPES['S2'], bytearray([page, (addr >> 8) & 0xFF, addr & 0xFF]), rec_data).print_srec() + '\r\n'
addr += len(rec_data) // 2
page_data = page_data[rec_len * 2:]
if len(records):
f.write(records)
# Add execution start address record
f.write(SRecord(STYPES['S8'], bytearray([0x00, 0xC0, 0x00])).print_srec() + '\r\n')
f.close()
sys.stdout.write("\r")
sys.stdout.flush()
LOG.info("Firmware ripped successfully")
def rip_pages(self, start, end, filepath):
last = end + 1
pages = last - start
# TODO: saving raw data is good enough?
f = open(filepath, 'a+')
for i, page in enumerate(xrange(start, last)):
progress = float(i) / pages
common.print_progress(progress)
self.__set_page(page)
f.write(self.__read_page())
f.close()
sys.stdout.write("\r")
sys.stdout.flush()
LOG.info("Firmware ripped successfully")
def rip_pages(self, start, end, filepath):
last = end + 1
pages = last - start
# TODO: saving raw data is good enough?
f = open(filepath, 'a+')
for i, page in enumerate(xrange(start, last)):
progress = float(i) / pages
common.print_progress(progress)
self.__set_page(page)
f.write(self.__read_page())
f.close()
sys.stdout.write("\r")
sys.stdout.flush()
LOG.info("Firmware ripped successfully")
def erase_pages(self, start, end):
total = end - start
last = end + 1
counter = 0
for page in xrange(start, last):
self.__set_page(page)
self.__erase_page()
if LOG.getEffectiveLevel() == logging.INFO:
progress = float(counter) / total
common.print_progress(progress)
counter += 1
if LOG.getEffectiveLevel() == logging.INFO:
sys.stdout.write("\r")
sys.stdout.flush()
LOG.info("Firmware erased successfully")
return True
def erase_pages(self, start, end):
total = end - start
last = end + 1
counter = 0
for page in xrange(start, last):
self.__set_page(page)
self.__erase_page()
if LOG.getEffectiveLevel() == logging.INFO:
progress = float(counter) / total
common.print_progress(progress)
counter += 1
if LOG.getEffectiveLevel() == logging.INFO:
sys.stdout.write("\r")
sys.stdout.flush()
LOG.info("Firmware erased successfully")
return True
def __get_consensus(ref, ref_name, align_file):
print 'Generating pile-up...'
index_allele_map = ['A', 'C', 'G', 'T']
allele_index_map = {
'A': 0,
'C': 1,
'G': 2,
'T': 3,
}
NONE = 'None'
# get consensus pile_up
consensus_pile = np.zeros((len(ref), 4), dtype=np.uint32)
with open(align_file, 'r') as alignment_file:
num_lines = float(sum((1 for line in alignment_file if not '>' in line)))
with open(align_file, 'r') as alignment_file:
line_count = 1.0
for line in alignment_file:
if '>' in line:
continue
alignment1, alignment2 = line.strip().split(',')
read1, position1 = alignment1.split(':')
read2, position2 = alignment2.split(':')
# if paired reads weren't mapped, continue
if position1 == NONE or position2 == NONE:
continue
# convert positions to ints
position1 = int(position1)
position2 = int(position2)
# if paired reads weren't mapped, continue
if position1 == -1 or position2 == -1:
continue
# if spacing between reads out of whack
# don't contribute to pile-up
MAX_GAP = 50
if position2 - position1 < 100 or position2 - position1 > 200:
continue
# contribute read1 to consensus pile
for i in xrange(len(read1)):
c = read1[i]
consensus_pile[position1 + i][allele_index_map[c]] += 1
# contribute read2 to consensus pile
for i in xrange(len(read2)):
c = read2[i]
consensus_pile[position2 + i][allele_index_map[c]] += 1
line_count += 1.0
progress = line_count / num_lines
cm.print_progress(progress)
cm.print_progress(1)
print '\tComplete'
# get consensus string from pileup
print 'Resolving consensus donor...'
consensus_file_name = cm.CONS_DIR + cm.CONS_PRE + ref_name + '.txt'
with open(consensus_file_name, 'w') as consensus_file:
consensus_file.write('>' + ref_name + '\n')
for i in xrange(len(consensus_pile)):
if i > 0 and i % 80 == 0:
consensus_file.write('\n')
msum = sum(consensus_pile[i])
max_pos = np.argmax(consensus_pile[i])
mmax = consensus_pile[i][max_pos]
# if it's a true max, write the consensus allele
if msum > 0 and float(mmax) / float(msum) > 0.25:
consensus_file.write(index_allele_map[max_pos])
else: # otherwise, stick with the ref allele (too much ambiguity)
consensus_file.write(ref[i])
cm.print_progress(float(i) / float(len(consensus_pile)))
cm.print_progress(1)
print '\tComplete'
return consensus_file_name
