def align_bwt(reads, index, count, ref_seq):
"""aligns a read to a reference genome
following the BWT index"""
best_aln = reads # contains alignments to report
for i in range(len(reads)): # for each one of the two ends
# try forward
read = best_aln[i].sequence
aln = perfect_match_bwt(read, index, count)
if aln != ".":
best_aln[i].strand = "+"
# try reverse
else:
read = u.rev(read)
aln = perfect_match_bwt(read, index, count)
if aln != ".":
best_aln[i].strand = "-"
# save positions
if aln != ".":
best_aln[i].aligned = True
best_aln[i].position = aln
SNPs, ins, dels, pos = 0, 0, 0, 0
# if one end is not aligned, try local alignment within the expected region of the genome
if best_aln[0].aligned and not best_aln[1].aligned:
eor1 = best_aln[0].position + len(best_aln[0].sequence)
refe_sl = ref_seq[eor1 + 75:eor1 + 175]
read_sl = best_aln[1].sequence if best_aln[0].strand == "-" else u.rev(
best_aln[1].sequence)
SNPs, ins, dels, pos = local_align(refe_sl, read_sl)
if SNPs != 0:
best_aln[1].mismatch = SNPs
best_aln[1].insertion = ins
best_aln[1].deletion = dels
best_aln[1].strand = "+" if best_aln[0].strand == "-" else "-"
best_aln[1].aligned = True
best_aln[1].position = pos + eor1 + 75
elif best_aln[1].aligned and not best_aln[0].aligned:
eor1 = best_aln[1].position
refe_sl = ref_seq[eor1 - 175:eor1 - 75]
read_sl = best_aln[0].sequence if best_aln[1].strand == "-" else u.rev(
best_aln[0].sequence)
SNPs, ins, dels, pos = local_align(refe_sl, read_sl)
if SNPs != 0:
best_aln[0].mismatch = SNPs
best_aln[0].insertion = ins
best_aln[0].deletion = dels
best_aln[0].strand = "+" if best_aln[1].strand == "-" else "-"
best_aln[0].aligned = True
best_aln[0].position = pos + eor1 - 175
# add to best alignments the information from the other end
best_aln[0].pair_position = best_aln[1].position
best_aln[0].pair_strand = best_aln[1].strand
best_aln[1].pair_position = best_aln[0].position
best_aln[1].pair_strand = best_aln[0].strand
return best_aln
def __init__(self, code=standard_cc):
self.nu = code[0]
self.g0 = util.rev(code[1], self.nu)
self.g1 = util.rev(code[2], self.nu)
self.output_map_1 = np.uint8(1 & (util.mul(self.g0, np.arange(1<<self.nu)) >> (self.nu-1)))
self.output_map_2 = np.uint8(1 & (util.mul(self.g1, np.arange(1<<self.nu)) >> (self.nu-1)))
self.states = np.arange(1<<self.nu)
self.state_inv_map = ((np.arange(1<<self.nu) << 1) & ((1<<self.nu)-1))[:,np.newaxis] + np.array([0,1])[np.newaxis,:]
self.state_inv_map_tag = np.tile(np.arange(1<<self.nu)[:,np.newaxis] >> (self.nu-1), (1,2))
self.output_map_1_soft = self.output_map_1.astype(int)[np.newaxis,:] * 2 - 1
self.output_map_2_soft = self.output_map_2.astype(int)[np.newaxis,:] * 2 - 1
def run(self):
update = False
try:
if self.registry.last_block:
current_prevhash = "%080x" % self.registry.last_block.hashPrevBlock
else:
current_prevhash = None
log.debug("Checking for new block.")
prevhash = util.rev((yield self.bitcoin_rpc.prevhash()))
if prevhash and prevhash != current_prevhash:
log.info("New block! Prevhash: %s" % prevhash)
update = True
elif Interfaces.timestamper.time(
) - self.registry.last_update >= settings.MERKLE_REFRESH_INTERVAL:
log.info("Merkle update! Prevhash: %s" % prevhash)
update = True
if update:
self.registry.update_block()
except Exception:
log.exception("UpdateWatchdog.run failed")
finally:
self.schedule()
def fill_from_rpc(self, data):
'''Convert getblocktemplate result into BlockTemplate instance'''
if 'height' not in data:
log.info("Waiting for new work...")
self.prevhash_hex = self.blank_hash
self.broadcast_args = self.build_fake_broadcast_args()
return
txhashes = [None] + [
util.ser_uint320(int(t['hash'], 16)) for t in data['transactions']
]
mt = merkletree.MerkleTree(txhashes)
self.height = data['height']
self.nVersion = data['version']
self.hashPrevBlock = int(data['previousblockhash'], 16)
self.nBits = int(data['bits'], 16)
self.nBitsHex = data['bits']
self.hashMerkleRoot = 0
self.nTime = 0
self.nNonce = 0
self.cbTxTime = int(self.timestamper.time())
self.nTxTime = self.cbTxTime * 1000
self.nHashCoin = 0
self.sigchecksum = 0
coinbase = CoinbaseTransaction(self.timestamper, self.coinbaser,
data['coinbasevalue'],
data['coinbaseaux']['flags'],
data['height'],
settings.COINBASE_EXTRAS, self.cbTxTime)
self.vtx = [
coinbase,
]
for tx in data['transactions']:
t = halfnode.CTransaction()
t.deserialize(StringIO.StringIO(binascii.unhexlify(tx['data'])))
self.vtx.append(t)
self.curtime = data['curtime']
self.timedelta = self.curtime - int(self.timestamper.time())
self.merkletree = mt
self.target = int((data['target']), 16)
log.info("Block height: %i network difficulty: %s" %
(self.height, self.diff_to_t(self.target)))
# Reversed prevhash
#self.prevhash_bin = binascii.unhexlify(util.reverse_hash_80(data['previousblockhash']))
self.prevhash_bin = binascii.unhexlify(
util.rev(data['previousblockhash']))
self.prevhash_hex = "%080x" % self.hashPrevBlock
#log.info("%s\n", repr(self))
self.broadcast_args = self.build_broadcast_args()
def submit_share(self, job_id, worker_name, session, extranonce1_bin, data,
difficulty):
job = self.get_job(job_id)
if job == None:
raise SubmitException("Job '%s' not found" % job_id)
ntime = util.flip(data[136:144])
if not job.check_ntime(int(ntime, 16)):
raise SubmitException("Ntime out of range")
if not job.register_submit(data):
log.info("Duplicate from %s, (%s %s)" % \
(worker_name, binascii.hexlify(extranonce1_bin), data))
raise SubmitException("Duplicate share")
hash_int = gapcoin_hash.getpowdiff(str(data))
block_hash_bin = util.doublesha(binascii.unhexlify(data[0:168]))
block_hash_hex = util.rev(binascii.hexlify(block_hash_bin))
'''log.info("block_hash_hex %s" % block_hash_hex)
log.info("shrint %s" % hash_int)
log.info("jobint %s" % job.target)%f
log.info("target %s" % difficulty)'''
if hash_int < difficulty:
raise SubmitException("Share less than target")
share_diff = float(float(hash_int) / float(pow(2, 48)))
if hash_int >= job.target:
log.info("BLOCK CANDIDATE! %s" % block_hash_hex)
extranonce2_bin = struct.pack('>L', 0)
#self.last_block.vtx[0].set_extranonce(extranonce1_bin + extranonce2_bin)
#txs = binascii.hexlify(util.ser_vector(self.last_block.vtx))
job.vtx[0].set_extranonce(extranonce1_bin + extranonce2_bin)
txs = binascii.hexlify(util.ser_vector(job.vtx))
serialized = str(data) + str(txs)
on_submit = self.bitcoin_rpc.submitblock(str(data), str(txs),
block_hash_hex)
if on_submit:
self.update_block()
return (block_hash_hex, share_diff, on_submit)
return (block_hash_hex, share_diff, None)
def fill_from_rpc(self, data):
'''Convert getblocktemplate result into BlockTemplate instance'''
txhashes = [None] + [ util.ser_uint256(int(t['hash'], 16)) for t in data['transactions'] ]
mt = merkletree.MerkleTree(txhashes)
coinbase = CoinbaseTransaction(self.timestamper, self.coinbaser, data['coinbasevalue'],
data['coinbaseaux']['flags'], data['height'],
settings.COINBASE_EXTRAS)
self.height = data['height']
self.nVersion = data['version']
self.hashPrevBlock = int(data['previousblockhash'], 16)
self.nBits = int(data['bits'], 16)
self.hashMerkleRoot = 0
self.nTime = 0
self.nNonce = 0
self.vtx = [ coinbase, ]
for tx in data['transactions']:
t = halfnode.CTransaction()
t.deserialize(StringIO.StringIO(binascii.unhexlify(tx['data'])))
self.vtx.append(t)
self.curtime = data['curtime']
self.timedelta = self.curtime - int(self.timestamper.time())
self.merkletree = mt
self.target = int(data['bits'], 16)
self.network_diff = round(float(self.target) / float(pow(2, 48)), 8)
log.info("Block: %i network difficulty: %0.8f" % (self.height, self.network_diff))
# Reversed prevhash
self.prevhash_bin = binascii.unhexlify(util.rev(data['previousblockhash']))
self.prevhash_hex = "%064x" % self.hashPrevBlock
self.broadcast_args = self.build_broadcast_args()
def parlindromic(s):
s = str(s)
if (s == rev(s)):
return True
else:
return False
def submit_share(self, job_id, worker_name, session, extranonce1_bin, extranonce2, ntime, nonce,
difficulty):
'''Check parameters and finalize block template. If it leads
to valid block candidate, asynchronously submits the block
back to the bitcoin network.
- extranonce1_bin is binary. No checks performed, it should be from session data
- job_id, extranonce2, ntime, nonce - in hex form sent by the client
- difficulty - decimal number from session, again no checks performed
- submitblock_callback - reference to method which receive result of submitblock()
'''
# Check if extranonce2 looks correctly. extranonce2 is in hex form...
if len(extranonce2) != self.extranonce2_size * 2:
raise SubmitException("Incorrect size of extranonce2. Expected %d chars" % (self.extranonce2_size*2))
# Check for job
job = self.get_job(job_id)
if job == None:
raise SubmitException("Job '%s' not found" % job_id)
# Check if ntime looks correct
if len(ntime) != 8:
raise SubmitException("Incorrect size of ntime. Expected 8 chars")
if not job.check_ntime(int(ntime, 16)):
raise SubmitException("Ntime out of range")
# Check nonce
if len(nonce) != 8:
raise SubmitException("Incorrect size of nonce. Expected 8 chars")
# Check for duplicated submit
if not job.register_submit(extranonce1_bin, extranonce2, ntime, nonce):
log.info("Duplicate from %s, (%s %s %s %s)" % \
(worker_name, binascii.hexlify(extranonce1_bin), extranonce2, ntime, nonce))
raise SubmitException("Duplicate share")
# Now let's do the hard work!
# ---------------------------
# 0. Some sugar
extranonce2_bin = binascii.unhexlify(extranonce2)
ntime_bin = binascii.unhexlify(ntime)
nonce_bin = binascii.unhexlify(nonce)
# 1. Build coinbase
coinbase_bin = job.serialize_coinbase(extranonce1_bin, extranonce2_bin)
coinbase_hash = util.doublesha(coinbase_bin)
# 2. Calculate merkle root
merkle_root_bin = job.merkletree.withFirst(coinbase_hash)
merkle_root_int = util.uint256_from_str(merkle_root_bin)
# 3. Serialize header with given merkle, ntime and nonce
header_bin = job.serialize_header(merkle_root_int, ntime_bin, nonce_bin)
# 4. Reverse header and compare it with target of the user
if settings.COINDAEMON_ALGO == 'scrypt':
hash_bin = ltc_scrypt.getPoWHash(''.join([ header_bin[i*4:i*4+4][::-1] for i in range(0, 20) ]))
elif settings.COINDAEMON_ALGO == 'scrypt-jane':
hash_bin = yac_scrypt.getPoWHash(''.join([ header_bin[i*4:i*4+4][::-1] for i in range(0, 20) ]), int(ntime, 16))
elif settings.COINDAEMON_ALGO == 'quark':
hash_bin = quark_hash.getPoWHash(''.join([ header_bin[i*4:i*4+4][::-1] for i in range(0, 20) ]))
elif settings.COINDAEMON_ALGO == 'skeinhash':
hash_bin = skeinhash.skeinhash(''.join([ header_bin[i*4:i*4+4][::-1] for i in range(0, 20) ]))
else:
hash_bin = util.doublesha(''.join([ header_bin[i*4:i*4+4][::-1] for i in range(0, 20) ]))
hash_int = util.uint256_from_str(hash_bin)
scrypt_hash_hex = "%064x" % hash_int
header_hex = binascii.hexlify(header_bin)
if settings.COINDAEMON_ALGO == 'scrypt' or settings.COINDAEMON_ALGO == 'scrypt-jane':
header_hex = header_hex+"000000800000000000000000000000000000000000000000000000000000000000000000000000000000000080020000"
elif settings.COINDAEMON_ALGO == 'quark':
header_hex = header_hex+"000000800000000000000000000000000000000000000000000000000000000000000000000000000000000080020000"
else: pass
target_user = self.diff_to_target(difficulty)
if hash_int > target_user:
raise SubmitException("Share is above target")
# Mostly for debugging purposes
target_info = self.diff_to_target(100000)
if hash_int <= target_info:
log.info("Yay, share with diff above 100000")
# Algebra tells us the diff_to_target is the same as hash_to_diff
share_diff = int(self.diff_to_target(hash_int))
on_submit = None
mm_submit = None
if settings.SOLUTION_BLOCK_HASH:
# Reverse the header and get the potential block hash (for scrypt only) only do this if we want to send in the block hash to the shares table
block_hash_bin = util.doublesha(''.join([ header_bin[i*4:i*4+4][::-1] for i in range(0, 20) ]))
block_hash_hex = block_hash_bin[::-1].encode('hex_codec')
# 5. Compare hash with target of the network
if hash_int <= job.target:
# Yay! It is block candidate!
log.info("We found a block candidate! %s" % scrypt_hash_hex)
# Reverse the header and get the potential block hash (for scrypt only)
#if settings.COINDAEMON_ALGO == 'scrypt' or settings.COINDAEMON_ALGO == 'sha256d':
# if settings.COINDAEMON_Reward == 'POW':
block_hash_bin = util.doublesha(''.join([ header_bin[i*4:i*4+4][::-1] for i in range(0, 20) ]))
block_hash_hex = block_hash_bin[::-1].encode('hex_codec')
#else: block_hash_hex = hash_bin[::-1].encode('hex_codec')
#else: block_hash_hex = hash_bin[::-1].encode('hex_codec')
# 6. Finalize and serialize block object
job.finalize(merkle_root_int, extranonce1_bin, extranonce2_bin, int(ntime, 16), int(nonce, 16))
if not job.is_valid():
# Should not happen
log.exception("FINAL JOB VALIDATION FAILED!(Try enabling/disabling tx messages)")
# 7. Submit block to the network
serialized = binascii.hexlify(job.serialize())
on_submit = self.bitcoin_rpc.submitblock(serialized, block_hash_hex, scrypt_hash_hex)
if on_submit:
self.update_block()
# 8. Compare hash with target of mm network
if hash_int <= job.mm_target:
log.info("We found a mm block candidate! %s" % scrypt_hash_hex)
coinbase_hex = binascii.hexlify(coinbase_bin)
branch_count = job.merkletree.branchCount()
branch_hex = job.merkletree.branchHex()
parent_hash = util.rev("%064x" % hash_int)
parent_header = util.flip(header_hex)
submission = coinbase_hex + parent_hash + branch_count + branch_hex + "000000000000000000" + parent_header;
mm_submit = self.mm_rpc.getauxblock(self.mm_hash,submission)
log.debug("Coinbase:%s",coinbase_hex)
log.debug("Branch Count:%s",branch_count)
log.debug("Branch Hex:%s",branch_hex)
log.debug("Parent Hash:%s",parent_hash)
log.debug("Parent Header:%s",parent_header)
log.debug("MM Hash:%s",self.mm_hash)
log.debug(" AuxPow:%s",submission)
log.debug(" Res:"+str(mm_submit))
if settings.SOLUTION_BLOCK_HASH:
return (header_hex, block_hash_hex, self.mm_hash, share_diff, on_submit, mm_submit)
else:
return (header_hex, scrypt_hash_hex, self.mm_hash, share_diff, on_submit, mm_submit)
def align_trivial(reads,
genome): # takes a list with two reads, and a ref genome
reference = genome.getSequence()[0] # for now takes only first chromosome
read1_fw = reads[0].sequence
read1_rv = u.rev(read1_fw)
read2_fw = reads[1].sequence
read2_rv = u.rev(read2_fw)
all_alng = {
0: [],
1: []
} # stores all valid alignments for each end of the read
best_aln = reads # contains alignments to report
d = 0 # max number of mismatches allowed when aligning
# iterate only once over regions of the genome of the size of the reads
for i in range(len(reference) - len(read1_fw) + 1):
ref = reference[i:(i + len(read1_fw))]
# check end_1
alignment = copy.deepcopy(reads[0])
# forward
diff = HammingDistance(read1_fw, ref, d)
if diff != None:
alignment.aligned = True
alignment.position = i
alignment.strand = "+"
alignment.mismatch = diff if len(diff) > 0 else ["."]
all_alng[0].append(alignment)
# reverse
else:
diff = HammingDistance(read1_rv, ref, d)
if diff != None:
alignment.aligned = True
alignment.position = i
alignment.strand = "-"
alignment.mismatch = diff if len(diff) > 0 else ["."]
all_alng[0].append(alignment)
# check end_2
alignment = copy.deepcopy(reads[1])
# forward
diff = HammingDistance(read2_fw, ref, d)
if diff != None:
alignment.aligned = True
alignment.position = i
alignment.strand = "+"
alignment.mismatch = diff if len(diff) > 0 else ["."]
all_alng[1].append(alignment)
# reverse
else:
diff = HammingDistance(read2_rv, ref, d)
if diff != None:
alignment.aligned = True
alignment.position = i
alignment.strand = "-"
alignment.mismatch = diff if len(diff) > 0 else ["."]
all_alng[1].append(alignment)
# check if there were any valid alignments for end_1
if len(all_alng[0]) > 0:
# from all valid alignments, get the best for end_1
best_aln[0] = all_alng[0][0]
for j in range(len(all_alng[0])):
if len(all_alng[0][j].mismatch) <= len(best_aln[0].mismatch):
best_aln[0] = all_alng[0][j]
# check if there were any valid alignments for end_2
if len(all_alng[1]) > 0:
# from all valid alignments, get the best for end_2
best_aln[1] = all_alng[1][0]
for j in range(len(all_alng[1])):
if len(all_alng[1][j].mismatch) <= len(best_aln[1].mismatch):
best_aln[1] = all_alng[1][j]
# add to best alignments the information from the other end
best_aln[0].pair_position = best_aln[1].position
best_aln[0].pair_strand = best_aln[1].strand
best_aln[1].pair_position = best_aln[0].position
best_aln[1].pair_strand = best_aln[0].strand
return best_aln
def submit_share(self, job_id, worker_name, session, extranonce1_bin,
extranonce2, ntime, nonce, difficulty):
'''Check parameters and finalize block template. If it leads
to valid block candidate, asynchronously submits the block
back to the bitcoin network.
- extranonce1_bin is binary. No checks performed, it should be from session data
- job_id, extranonce2, ntime, nonce - in hex form sent by the client
- difficulty - decimal number from session, again no checks performed
- submitblock_callback - reference to method which receive result of submitblock()
'''
# Check if extranonce2 looks correctly. extranonce2 is in hex form...
if len(extranonce2) != self.extranonce2_size * 2:
raise SubmitException(
"Incorrect size of extranonce2. Expected %d chars" %
(self.extranonce2_size * 2))
# Check for job
job = self.get_job(job_id)
if job == None:
raise SubmitException("Job '%s' not found" % job_id)
# Check if ntime looks correct
if len(ntime) != 8:
raise SubmitException("Incorrect size of ntime. Expected 8 chars")
if not job.check_ntime(int(ntime, 16)):
raise SubmitException("Ntime out of range")
# Check nonce
if len(nonce) != 8:
raise SubmitException("Incorrect size of nonce. Expected 8 chars")
# Check for duplicated submit
if not job.register_submit(extranonce1_bin, extranonce2, ntime, nonce):
log.info("Duplicate from %s, (%s %s %s %s)" % \
(worker_name, binascii.hexlify(extranonce1_bin), extranonce2, ntime, nonce))
raise SubmitException("Duplicate share")
# Now let's do the hard work!
# ---------------------------
# 0. Some sugar
extranonce2_bin = binascii.unhexlify(extranonce2)
ntime_bin = binascii.unhexlify(ntime)
nonce_bin = binascii.unhexlify(nonce)
# 1. Build coinbase
coinbase_bin = job.serialize_coinbase(extranonce1_bin, extranonce2_bin)
coinbase_hash = util.doublesha(coinbase_bin)
# 2. Calculate merkle root
merkle_root_bin = job.merkletree.withFirst(coinbase_hash)
merkle_root_int = util.uint256_from_str(merkle_root_bin)
# 3. Serialize header with given merkle, ntime and nonce
header_bin = job.serialize_header(merkle_root_int, ntime_bin,
nonce_bin)
# 4. Reverse header and compare it with target of the user
if settings.COINDAEMON_ALGO == 'scrypt':
hash_bin = ltc_scrypt.getPoWHash(''.join(
[header_bin[i * 4:i * 4 + 4][::-1] for i in range(0, 20)]))
elif settings.COINDAEMON_ALGO == 'scrypt-jane':
hash_bin = yac_scrypt.getPoWHash(
''.join(
[header_bin[i * 4:i * 4 + 4][::-1] for i in range(0, 20)]),
int(ntime, 16))
elif settings.COINDAEMON_ALGO == 'quark':
hash_bin = quark_hash.getPoWHash(''.join(
[header_bin[i * 4:i * 4 + 4][::-1] for i in range(0, 20)]))
elif settings.COINDAEMON_ALGO == 'skeinhash':
hash_bin = skeinhash.skeinhash(''.join(
[header_bin[i * 4:i * 4 + 4][::-1] for i in range(0, 20)]))
else:
hash_bin = util.doublesha(''.join(
[header_bin[i * 4:i * 4 + 4][::-1] for i in range(0, 20)]))
hash_int = util.uint256_from_str(hash_bin)
scrypt_hash_hex = "%064x" % hash_int
header_hex = binascii.hexlify(header_bin)
if settings.COINDAEMON_ALGO == 'scrypt' or settings.COINDAEMON_ALGO == 'scrypt-jane':
header_hex = header_hex + "000000800000000000000000000000000000000000000000000000000000000000000000000000000000000080020000"
elif settings.COINDAEMON_ALGO == 'quark':
header_hex = header_hex + "000000800000000000000000000000000000000000000000000000000000000000000000000000000000000080020000"
else:
pass
target_user = self.diff_to_target(difficulty)
if hash_int > target_user:
raise SubmitException("Share is above target")
# Mostly for debugging purposes
target_info = self.diff_to_target(100000)
if hash_int <= target_info:
log.info("Yay, share with diff above 100000")
# Algebra tells us the diff_to_target is the same as hash_to_diff
share_diff = int(self.diff_to_target(hash_int))
on_submit = None
mm_submit = None
if settings.SOLUTION_BLOCK_HASH:
# Reverse the header and get the potential block hash (for scrypt only) only do this if we want to send in the block hash to the shares table
block_hash_bin = util.doublesha(''.join(
[header_bin[i * 4:i * 4 + 4][::-1] for i in range(0, 20)]))
block_hash_hex = block_hash_bin[::-1].encode('hex_codec')
# 5. Compare hash with target of the network
if hash_int <= job.target:
# Yay! It is block candidate!
log.info("We found a block candidate! %s" % scrypt_hash_hex)
# Reverse the header and get the potential block hash (for scrypt only)
#if settings.COINDAEMON_ALGO == 'scrypt' or settings.COINDAEMON_ALGO == 'sha256d':
# if settings.COINDAEMON_Reward == 'POW':
block_hash_bin = util.doublesha(''.join(
[header_bin[i * 4:i * 4 + 4][::-1] for i in range(0, 20)]))
block_hash_hex = block_hash_bin[::-1].encode('hex_codec')
#else: block_hash_hex = hash_bin[::-1].encode('hex_codec')
#else: block_hash_hex = hash_bin[::-1].encode('hex_codec')
# 6. Finalize and serialize block object
job.finalize(merkle_root_int, extranonce1_bin, extranonce2_bin,
int(ntime, 16), int(nonce, 16))
if not job.is_valid():
# Should not happen
log.exception(
"FINAL JOB VALIDATION FAILED!(Try enabling/disabling tx messages)"
)
# 7. Submit block to the network
serialized = binascii.hexlify(job.serialize())
on_submit = self.bitcoin_rpc.submitblock(serialized,
block_hash_hex,
scrypt_hash_hex)
if on_submit:
self.update_block()
# 8. Compare hash with target of mm network
if hash_int <= job.mm_target:
log.info("We found a mm block candidate! %s" % scrypt_hash_hex)
coinbase_hex = binascii.hexlify(coinbase_bin)
branch_count = job.merkletree.branchCount()
branch_hex = job.merkletree.branchHex()
parent_hash = util.rev("%064x" % hash_int)
parent_header = util.flip(header_hex)
submission = coinbase_hex + parent_hash + branch_count + branch_hex + "000000000000000000" + parent_header
mm_submit = self.mm_rpc.getauxblock(self.mm_hash, submission)
log.debug("Coinbase:%s", coinbase_hex)
log.debug("Branch Count:%s", branch_count)
log.debug("Branch Hex:%s", branch_hex)
log.debug("Parent Hash:%s", parent_hash)
log.debug("Parent Header:%s", parent_header)
log.debug("MM Hash:%s", self.mm_hash)
log.debug(" AuxPow:%s", submission)
log.debug(" Res:" + str(mm_submit))
if settings.SOLUTION_BLOCK_HASH:
return (header_hex, block_hash_hex, self.mm_hash, share_diff,
on_submit, mm_submit)
else:
return (header_hex, scrypt_hash_hex, self.mm_hash, share_diff,
on_submit, mm_submit)
def pileup(aligns, ref_genome):
"""take a file with aligned reads and extract variants."""
print("Generating Pileup from file: ")
print(" " + aligns)
# open aligned reads file, and pileup file
reads_f = open(aligns, 'r')
pileup_f = open(aligns + ".plp", "w")
# set variables
genome = ref_genome.getSequence()[0]
pile = [0] * len(genome)
sym = {"A": 0, "C": 1, "G": 2, "T": 3}
let = {0: "A", 1: "C", 2: "G", 3: "T"}
donor = [list(pile), list(pile), list(pile), list(pile)]
end = False # flag for end of reads
window = 1000 # size of the window to slide
# write with the expected format
pileup_f.write(">" + list(ref_genome.genome.keys())[0] + "\n")
pileup_f.write(">SNP\n")
start = 0
reads = []
# keep function running while there are reads in file
while not end:
# collect the information of all the reads inside the window
for read in reads_f:
read = read.strip().split('\t')
seq, init, pos = read[0], int(read[3]), read[2]
if pos == "-":
seq = u.rev(seq) # reverse if inverted
reads.append((seq, init)) # save the read
if init >= start + window: # stop with the first that scapes
break # the end of the window
for read in reads:
seq = read[0] # retrieve the reads from array
init = read[1]
for i in range(len(seq)): # position by position of each read
donor[sym[seq[i]]][init + i] += 1 # add to PILEUP!
# call variants:
depth = 0
dom = 0
final = min(len(genome), start + window)
for j in range(start, final): # for each position in the window ...
don = genome[j] # by default, the donor is = to reference
for nt in range(4): # for each nucleotide... (ACGT)
depth += donor[nt][j] # add to sequencing depth for position j
if dom < donor[nt][j]:
dom = donor[nt][
j] # save the max depth for any nucleotide in pos j
don = let[nt] # and the identity of that nucleotide
if don != genome[j]: # if donor and reference diverge...
if depth > 2: # QC: and donor has >2 reads
if float(dom) / float(
depth) > 0.6: # QC: and freq(nt) >0.6
#print(genome[j],donor[0][j],donor[1][j],donor[2][j],donor[3][j],don,j)
pileup_f.write(genome[j] + "," + don + "," + str(j) +
"\n")
depth = 0
dom = 0
print(len(reads))
# reset variables or finish outputing
if len(genome) > start + window:
start += window
reads = []
else:
end = True
pileup_f.close()
return 1
def plcp_bits(rate, octets):
plcp_rate = util.rev(rate.encoding, 4)
plcp = plcp_rate | (octets << 5)
parity = (util.mul(plcp, 0x1FFFF) >> 16) & 1
plcp |= parity << 17
return util.shiftout(np.array([plcp]), 18)
data = sym[ofdm.format.dataSubcarriers]
pilots = sym[ofdm.format.pilotSubcarriers] * next(pilotPolarity) * ofdm.format.pilotTemplate
kalman_u = kalman_state.update(np.sum(pilots))
data *= kalman_u
pilots *= kalman_u
if i==0: # signal
signal_bits = data.real>0
signal_bits = interleaver.interleave(signal_bits, ofdm.format.Nsc, 1, reverse=True)
scrambled_plcp_estimate = code.decode(signal_bits*2-1, 18)
plcp_estimate = scrambler.scramble(scrambled_plcp_estimate, int(ofdm.format.Nsc*.5), scramblerState=0)
parity = (np.sum(plcp_estimate) & 1) == 0
if not parity:
return None, None, 0
plcp_estimate = util.shiftin(plcp_estimate[:18], 18)[0]
try:
encoding_estimate = util.rev(plcp_estimate & 0xF, 4)
rate_estimate = [r.encoding == encoding_estimate for r in wifi_802_11_rates].index(True)
except ValueError:
return None, None, 0
r_est = wifi_802_11_rates[rate_estimate]
Nbpsc, constellation_estimate = r_est.Nbpsc, r_est.constellation
Ncbps, Nbps = r_est.Ncbps, r_est.Nbps
length_octets = (plcp_estimate >> 5) & 0xFFF
length_bits = length_octets * 8
length_coded_bits = (length_bits+16+6)*2
length_symbols = (length_coded_bits+Ncbps-1) // Ncbps
signal_bits = code.encode(scrambled_plcp_estimate)
dispersion = data - qam.bpsk.symbols[interleaver.interleave(signal_bits, ofdm.format.Nsc, 1)]
dispersion = np.var(dispersion)
else:
if drawingCalls is not None:
def pileup(aligns, ref_genome):
"""take a file with aligned reads and extract variants."""
print("Generating Pileup from file: ")
print(" " + aligns)
# open aligned reads file, and pileup file
reads_f = open(aligns, 'r')
# set variables
genome = ref_genome.getSequence()[0]
snps = {}
dels = {} # format: key=position, vals=(ref, (alt,) support)
insr = {}
# collect the information of all the reads inside the window
for read in reads_f:
read = read.strip().split('\t')
seq, init, pos = read[0], int(read[3]), read[2]
if pos == "-":
seq = u.rev(seq) # reverse if inverted
# get differences if any:
# SNPs
if read[4] != ".":
for i in map(int, read[4].split(",")):
# add support if it exists (position and allele)
if (init + i) in snps:
if seq[i] == snps[init + i][1]:
# pos_on_ref ref_allele alt_allele support +1
snps[init + i] = (genome[init + i], seq[i],
(snps[init + i][2] + 1))
else: # or create the event if it doesn't
snps[init + i] = (genome[init + i], seq[i], 1)
# deletions
if read[5] != ".":
pos_d = list(map(int, read[5].split(",")))
ale_d = list(map(int, read[6].split(",")))
for i in range(len(pos_d)):
pi_del = init + pos_d[i] + 1
pf_del = init + pos_d[i] + 1 + ale_d[i]
# add support if it exists (position and allele)
if pi_del in dels:
if dels[pi_del][0] == genome[pi_del:pf_del]:
dels[pi_del][1] += 1
else: # or create the event if it doesn't
dels[pi_del] = [genome[pi_del:pf_del], 1]
# insertions
if read[7] != ".":
pos_i = list(map(int, read[7].split(",")))
ale_i = list(map(int, read[8].split(",")))
for i in range(len(pos_i)):
pi_ins = pos_i[i] + 1
pf_ins = pos_i[i] + 1 + ale_i[i]
p_geno = pos_i[i] + 1 + init
# add support if it exists (position and allele)
if p_geno in insr:
if insr[p_geno][0] == seq[pi_ins:pf_ins]:
insr[p_geno][1] += 1
else: # or create the event if it doesn't
insr[p_geno] = [seq[pi_ins:pf_ins], 1]
# write with the expected format
pileup_f = open(aligns + ".plp", "w")
pileup_f.write(">" + list(ref_genome.genome.keys())[0] + "\n")
pileup_f.write(">INS\n")
insr_pos = list(insr.keys())
insr_pos.sort()
for j in insr_pos:
if insr[j][1] > 2:
pileup_f.write(insr[j][0] + "," + str(j) + "\n")
pileup_f.write(">DEL\n")
dels_pos = list(dels.keys())
dels_pos.sort()
for j in dels_pos:
if dels[j][1] > 2:
pileup_f.write(dels[j][0] + "," + str(j) + "\n")
pileup_f.write(">SNP\n")
snps_pos = list(snps.keys())
snps_pos.sort()
for j in snps_pos:
if snps[j][2] > 3:
pileup_f.write(snps[j][0] + "," + snps[j][1] + "," + str(j) + "\n")
pileup_f.close()
return 1
def submit_share(self, job_id, worker_name, session, extranonce1_bin,
extranonce2, ntime, nonce, difficulty):
# Check for job
job = self.get_job(job_id)
if job == None:
raise SubmitException("Job '%s' not found" % job_id)
nonce = util.rev(nonce)
ntime = util.rev(ntime)
extranonce2_bin = binascii.unhexlify(extranonce2)
ntime_bin = binascii.unhexlify(ntime)
nonce_bin = binascii.unhexlify(nonce)
# Check if extranonce2 looks correctly. extranonce2 is in hex form...
if len(extranonce2) != self.extranonce2_size * 2:
raise SubmitException(
"Incorrect size of extranonce2. Expected %d chars" %
(self.extranonce2_size * 2))
# Check if ntime looks correct
if len(ntime) != 8:
raise SubmitException("Incorrect size of ntime. Expected 8 chars")
if not job.check_ntime(int(ntime, 16)):
raise SubmitException("Ntime out of range")
# Check nonce
if len(nonce) != 8:
raise SubmitException("Incorrect size of nonce. Expected 8 chars")
# Check for duplicated submit
if not job.register_submit(extranonce1_bin, extranonce2, ntime, nonce):
log.info("Duplicate from %s, (%s %s %s %s)" % \
(worker_name, binascii.hexlify(extranonce1_bin), extranonce2, ntime, nonce))
raise SubmitException("Duplicate share")
# 1. Build coinbase
coinbase_bin = job.serialize_coinbase(extranonce1_bin, extranonce2_bin)
coinbase_hash = kshake320_hash.getHash320(coinbase_bin)
# 2. Calculate merkle root
merkle_root_bin = job.merkletree.withFirst(coinbase_hash)
merkle_root_int = util.uint320_from_str(merkle_root_bin)
# 3. Serialize header with given merkle, ntime and nonce
header_bin = job.serialize_header(merkle_root_bin, int(ntime, 16),
int(nonce, 16))
header_hex = binascii.hexlify(header_bin)
header_hex = header_hex + "0000000000000000"
# 4. Reverse header and compare it with target of the user
hash_bin = kshake320_hash.getPoWHash(header_bin)
hash_int = util.uint320_from_str(hash_bin)
hash_hex = "%080x" % hash_int
block_hash_hex = hash_bin[::-1].encode('hex_codec')
target_user = float(self.diff_to_target(difficulty))
if hash_int > target_user:
log.info("ABOVE TARGET!")
raise SubmitException("Share above target")
target_info = self.diff_to_target(50)
if hash_int <= target_info:
log.info("YAY, share with diff above 50")
# Algebra tells us the diff_to_target is the same as hash_to_diff
share_diff = float(self.diff_to_target(hash_int))
if hash_int <= job.target:
# Yay! It is block candidate!
log.info("BLOCK CANDIDATE! %s" % block_hash_hex)
# Finalize and serialize block object
job.finalize(merkle_root_int, extranonce1_bin, extranonce2_bin,
int(ntime, 16), int(nonce, 16))
if not job.is_valid():
# Should not happen
log.info("FINAL JOB VALIDATION FAILED!")
# Submit block to the network
'''serialized = binascii.hexlify(job.serialize())
on_submit = self.bitcoin_rpc.submitblock(str(serialized), block_hash_hex)'''
job.vtx[0].set_extranonce(extranonce1_bin + extranonce2_bin)
txs = binascii.hexlify(util.ser_vector(job.vtx))
on_submit = self.bitcoin_rpc.submitblock_wtxs(
str(header_hex), str(txs), block_hash_hex)
'''if on_submit:
self.update_block()'''
return (block_hash_hex, share_diff, on_submit)
return (block_hash_hex, share_diff, None)