def rank_with_paired_nn(dicta, queries, model_path, model_opt_path):
"""
Rank clean dictionary chunks for each noisy query chunk using the paired
(clean,noisy) input neural network
"""
with open(model_path, 'rb') as fmodel:
ml = load(fmodel)
model_func = ml.model.get_theano_function()
npz = np.load(model_opt_path)
queries = queries.astype(np.float32)
dicta = dicta.astype(np.float32)
T = queries.shape[0]
D = queries.shape[0]
sim = np.zeros((D, T))
for t in xrange(T):
sys.write('.')
if t % 70 == 0 and t:
sys.write('\n')
qrep = repmat(queries[t, :], D, 1)
test_x = np.hstack([dicta, qrep])
test_x = mean_var_normalize_test(test_x, npz['train_mean'], npz['train_std'])
sim[:, t] = model_func(test_x)
best_chunks = np.argmax(sim, axis=0)
return best_chunks
def handle_data(self, message):
payload = msgpack.unpackb(message)
if 'connect' in payload:
host, port_str = payload['connect'].split('::')
port = int(port_str)
self._sock = socket.socket()
self._sock.connect((host, port))
response = msgpack.packb({'type': 'STATUS',
'value': 'OPEN'})
self._send(response)
eventlet.spawn(self._reader)
elif 'close' in payload:
self._sock.close()
status = msgpack.packb({'type': 'STATUS',
'value': 'CLOSED'})
self._send(status)
elif 'content' in payload:
try:
self._sock.send(payload['content'])
except Exception as exc:
print exc
self._sock.close()
else:
message = 'Unknown payload type: {}\n'.format(payload.type)
sys.write(message)
def main():
global possible_subnet_list
global targets
global port
global args
# Check if they want to use a file of addresses
if(args.addfile == None):
# Calculate non-file address
if(args.address == None):
with print_lock:
sys.stderr.write(bad_n + "need an address to work with (-a)\nExiting...\n")
exit(403)
else:
# Calculate addresses
populate_address(args.address)
# Use address file instead
else:
try:
with open(args.addfile,"r") as targs:
with print_lock:
sys.stdout.write(notify + "running with address file!\n")
for line in targs:
populate_address(line)
targs.close()
except:
with print_lock:
sys.write(bad + "could not open that file.")
exit()
# Remove blank list entries. <3 nano users
possible_subnet_list = list(filter(None, possible_subnet_list))
# EXIT FOR TESTING
if(args.test == True):
print(possible_subnet_list)
exit()
# Feed the thread monsters
for address_index in range(0,len(possible_subnet_list)):
q.put(address_index)
q.join()
# Report if no hosts were up
if None in targets:
with print_lock:
sys.stderr.write(bad_n + "No SSH found!\nExiting...\n")
exit(404)
if(args.o != None):
with print_lock:
sys.stdout.write(notify + "Writing found targets to {}\n".format(args.o))
f = open(args.o,"w+")
for t in targets:
f.write(t + "\n")
f.close()
with print_lock:
sys.stdout.write("\nThat's all I can do!\n")
print("Attack lasted {:.2f} seconds!".format(time.time() - start))
def check_size(self, out, image):
value = self.config_entry_image.get('check-size')
if not value:
return 0
dtb_size = 0
if self.config_entry_image.get('check-size-with-dtb'):
for dtb in glob.glob(
os.path.join(self.dir, 'arch',
self.config_entry_base['kernel-arch'],
'boot/dts/*.dtb')):
dtb_size = max(dtb_size, os.stat(dtb).st_size)
size = os.stat(image).st_size + dtb_size
if size > value:
out.write('Image too large (%d > %d)! Refusing to continue.\n' % (size, value))
return 1
# 1% overhead is desirable in order to cope with growth
# through the lifetime of a stable release. Warn if this is
# not the case.
usage = (float(size)/value) * 100.0
out.write('Image size %d/%d, using %.2f%%. ' % (size, value, usage))
if size > value:
sys.write('Too large. Refusing to continue.\n')
return 1
elif usage >= 99.0:
out.write('Under 1%% space in %s. ' % self.changelog.distribution)
else:
out.write('Image fits. ')
out.write('Continuing.\n')
return 0
def main():
usage = "usage: %prog [options] bamfile \n generate a shell script that generates locus specific BAM file of a certain window size around bed coordinates for a given orignal BAM file\n\n"
parser = OptionParser(usage)
parser.add_option("--bedfile", type="string", dest="bedfile", help="bedfile")
parser.add_option("--upstreampad", type="int", default=100, dest="upstream", help="upstream" )
parser.add_option("--downstreampad", type="int", default=100, dest="downstream", help="downstream" )
parser.add_option("--ref", type="string", default="human_reference_v37.fa", dest="ref", help="name of reference assembly (fasta) file (.fa)")
parser.add_option("--bamprefix", type="string", default=None, dest="bamprefix", help="output prefix of bam file")
(options, args)=parser.parse_args()
if options.bamprefix == None:
sys.write("please provide a value to --bamprefix option!\n ")
sys.exit(1)
bamfile=args[0]
if os.path.isfile(bamfile) == False:
sys.stderr.write("bam file doesn't exists! " + bamfile +"\n")
sys.exit(1)
bamindexfile=bamfile+".bai"
if os.path.isfile(bamindexfile) == False:
sys.stderr.write("bam index file doesn't exist! did you run samtools/bamtools index?\n")
sys.exit(1)
if os.path.isfile(options.bedfile) == False:
sys.stderr.write("bed file doesn't exist! " + options.bedfile + "\n")
exit(1)
bam = pysam.Samfile( bamfile, "rb" )
bedfh=open(options.bedfile, 'r')
for coord_tuple in yield_bedcoordinate(bedfh):
(chr, start, end)=coord_tuple
regionstring=chr+":"+start+".."+end
regionstring=":".join( [ chr, str( int(start)-options.upstream), str( int(end)+options.downstream ) ])
bamfilename=".".join( [ options.bamprefix, regionstring, 'bam' ] )
#now create a bamfile for the region defined by the bed coordinate, plus/minus the pad
#the bamfile is names as bamfileprefix.regionstring.bam
outbam = pysam.Samfile(bamfilename, "wb", template=bam)
print coord_tuple
print chr, str( int(start)-options.upstream) , str( int(end)+options.downstream )
#now for each aligned read in the region, write it to the bam file
for alignedread in bam.fetch( chr, int(start)-options.upstream, int(end)+options.downstream ):
if alignedread.is_paired:
outbam.write(alignedread)
outbam.close()
bam.close()
def get(self):
prefix = self.get_argument('q')
if prefix is None:
sys.stderr.write('[ERROR] no name')
sys.write('error')
return
sugg_info = _sugg_server.get_sugg(prefix.encode('utf-8'))
self.render("sugg.html", info=sugg_info)
def main():
parser = argparse.ArgumentParser(description="")
parser.add_argument('-compile_commands',
default='compile_commands.json',
help='location of binary to use for clang-format')
parser.add_argument('-binary',
help='location of binary to use for clang-format')
parser.add_argument('-output',
default='clang-format-result.diff',
help='output file')
args = parser.parse_args()
if not args.binary:
for ext in ["", "-6.0", "-7.0", "-8.0", "-9.0"]:
if test_cmd(["clang-format" + ext, "--version"]):
args.binary = "clang-format" + ext
break
else:
sys.stdout.write(
"Could not find clang format please use the '-binary'\n")
sys.exit(1)
with open(args.compile_commands) as f:
data = json.load(f)
with open(args.output, 'w') as out:
for item in data:
filename = item['file']
command = [args.binary, filename]
p = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True)
formatted_code, err = p.communicate()
if p.returncode != 0:
sys.write(err)
sys.exit(p.returncode)
with open(filename) as f:
code = f.read().split('\n')
diff = difflib.unified_diff(code, formatted_code.split('\n'),
filename + " (original)",
filename + " (formatted)", '', '', 3,
"")
diff_string = '\n'.join(diff)
if len(diff_string) > 0:
sys.stdout.write("\n\nWarning: Inconsistent format " +
filename + "\n")
sys.stdout.write(diff_string)
out.write("\n\nWarning: Inconsistent format " + filename +
"\n")
out.write(diff_string)
def parse_mod_data(args):
if VERBOSE: sys.stderr.write('Reading megalodon data\n')
try:
mod_dat = pd.read_csv(mh.get_megalodon_fn(args.megalodon_results_dir,
mh.PR_MOD_TXT_NAME),
sep='\t')
except FileNotFoundError:
sys.write('ERROR: Must provide a valid Megalodon result directory.')
sys.exit(1)
return mod_dat
def printMap(nMap):
for i in size(nMap, 0) :
for j in size(nMap, 1):
if nMap[i,j] == 0:
sys.write('*')
elif nMap[i,j] == 1:
sys.write('c')
else:
sys.write('.')
sys.write('\n')
sys.write('\n')
def pcToSystem(file): #Recibimos el archivo ya abierto listo para ser leído desde nuestra pc
sys=open("fiunamfs.img","rw")
sys.seek(1024)
for i in range(64):
if sys.read(15)=='AQUI_NO_VA_NADA': #Leemos un espacio vacío
#Leemos el inicio del espacio
sys.seek(sys.tell()+10)
ini=int(sys.read(5))
sys.write(file.read()) #Copiamos la informacion
fin=int(sys.tell())
sys.seek(ini)
sys.seek(sys.tell()-14)
sys.write(ini-fin) #guardamos el tamaño del archivo
else:
sys.seek(sys.tell()+49)
sys.close()
file.close()
def systemToPC(nombre, ruta): #recibimos el nombre del archivo y la ruta
sys=open("fiunamfs.img","rw")
sys.seek(1024)
for i in range(64):
if sys.read(15)==nombre: #Leemos un espacio vacío
#Leemos el inicio del espacio
sys.seek(sys.tell()+10)
ini=int(sys.read(5))
#Crear objeto archivo nuevo en la ruta dada y copiar en él la información
fin=int(sys.tell())
sys.seek(ini)
sys.seek(sys.tell()-14)
sys.write(ini-fin) #guardamos el tamaño del archivo
else:
sys.seek(sys.tell()+49)
sys.close()
file.close()
def parse_jobs(self, jobs_str):
job_info = {}
job_strs = jobs_str.split(' ')
for job_str in job_strs:
if '(' in job_str:
job_id, info_str = job_str.split('(')
job_info[job_id] = {}
info_strs = info_str[:-2]
for info_str in info_strs.split(','):
try:
key, value = info_str.split('=')
job_info[job_id][key] = value
except ValueError:
if self._is_verbose:
msg = '### warnig: no value for {0}\n'
sys.write(msg.format(key))
job_info[job_id][info_str] = None
return job_info
def parse_jobs(self, jobs_str):
job_info = {}
job_strs = jobs_str.split(' ')
for job_str in job_strs:
if '(' in job_str:
job_id, info_str = job_str.split('(')
job_info[job_id] = {}
info_strs = info_str[:-2]
for info_str in info_strs.split(','):
try:
key, value = info_str.split('=')
job_info[job_id][key] = value
except ValueError:
if self._is_verbose:
msg = '### warnig: no value for {0}\n'
sys.write(msg.format(key))
job_info[job_id][info_str] = None
return job_info
def paste(
self,
fname,
req_title=None,
req_language=None,
req_password=None,
req_private=None,
req_expire=30,
req_project=None,
):
fargs = locals()
endpoint = "/create"
params = {"language": "text", "title": os.path.basename(fname)}
try:
fp = open(fname, "r")
params["data"] = fp.read() # ugh, how about some cap hu?
except Exception, e:
sys.write(sys.stderr, "Failed to open paste file {}: {}".format(fname, e))
return
def doc_changed(self, *args):
if self.live_coding_enabled and self.bot:
doc = self.window.get_active_document()
source = self.get_source(doc)
try:
self.bot.live_source_load(source)
except Exception:
self.bot = None
self.disconnect_change_handler(doc)
raise
except IOError as e:
self.bot = None
self.disconnect_change_handler()
if e.errno == errno.EPIPE:
# EPIPE error
sys.write('FIXME: %s\n' % str(e))
else:
# Something else bad happened
raise
def run_jobs(self, stream=sys.stdout, resubmit_failed=False):
"""Function to dipatch jobs and collect results
Parameters
-----------
stream : `file`
Stream that this function will print to,
Must have 'write' function.
resubmit_failed : bool
Resubmit failed jobs.
Returns
-------
status_vect : `JobStatusVector`
Vector that summarize the number of jobs in various states.
"""
self._build_job_dict()
self._interface._dry_run = self.args['dry_run']
scatter_status = self._interface.submit_jobs(
self.scatter_link, job_archive=self._job_archive, stream=stream)
if scatter_status == JobStatus.failed:
return JobStatus.failed
status_vect = self.check_status(stream, write_status=True)
status = status_vect.get_status()
if status == JobStatus.partial_failed:
if resubmit_failed:
sys.write("Resubmitting partially failed link %s\n" %
self.full_linkname)
status_vect = self.resubmit(stream=stream,
fail_running=False,
resubmit_failed=True)
else:
sys.stdout.write(
"NOT resubmitting partially failed link %s\n" %
self.full_linkname)
return status_vect
def paste(self,
fname,
req_title=None,
req_language=None,
req_password=None,
req_private=None,
req_expire=30,
req_project=None):
fargs = locals()
endpoint = '/create'
params = {
'language': 'text',
'title': os.path.basename(fname),
}
try:
fp = open(fname, 'r')
params['data'] = fp.read() # ugh, how about some cap hu?
except Exception, e:
sys.write(sys.stderr,
'Failed to open paste file {}: {}'.format(fname, e))
return
def run_jobs(self, stream=sys.stdout, resubmit_failed=False):
"""Function to dipatch jobs and collect results
Parameters
-----------
stream : `file`
Stream that this function will print to,
Must have 'write' function.
resubmit_failed : bool
Resubmit failed jobs.
Returns
-------
status_vect : `JobStatusVector`
Vector that summarize the number of jobs in various states.
"""
self._build_job_dict()
self._interface._dry_run = self.args['dry_run']
scatter_status = self._interface.submit_jobs(self.scatter_link,
job_archive=self._job_archive,
stream=stream)
if scatter_status == JobStatus.failed:
return JobStatus.failed
status_vect = self.check_status(stream, write_status=True)
status = status_vect.get_status()
if status == JobStatus.partial_failed:
if resubmit_failed:
sys.write("Resubmitting partially failed link %s\n" %
self.full_linkname)
status_vect = self.resubmit(stream=stream, fail_running=False, resubmit_failed=True)
else:
sys.stdout.write("NOT resubmitting partially failed link %s\n" %
self.full_linkname)
return status_vect
def check_size(self, out, image):
value = self.config_entry_image.get('check-size')
if not value:
return 0
dtb_size = 0
if self.config_entry_image.get('check-size-with-dtb'):
for dtb in glob.glob(
os.path.join(self.dir, 'arch',
self.config_entry_base['kernel-arch'],
'boot/dts/*.dtb')):
dtb_size = max(dtb_size, os.stat(dtb).st_size)
size = os.stat(image).st_size + dtb_size
if size > value:
out.write('Image too large (%d > %d)! Refusing to continue.\n' %
(size, value))
return 1
# 1% overhead is desirable in order to cope with growth
# through the lifetime of a stable release. Warn if this is
# not the case.
usage = (float(size) / value) * 100.0
out.write('Image size %d/%d, using %.2f%%. ' % (size, value, usage))
if size > value:
sys.write('Too large. Refusing to continue.\n')
return 1
elif usage >= 99.0:
out.write('Under 1%% space in %s. ' % self.changelog.distribution)
else:
out.write('Image fits. ')
out.write('Continuing.\n')
return 0
def main():
usage = "usage: %prog [options] bamfile \n generate a shell script that generates locus specific BAM file of a certain window size around bed coordinates for a given orignal BAM file\n\n"
parser = OptionParser(usage)
parser.add_option("--bedfile",
type="string",
dest="bedfile",
help="bedfile")
parser.add_option("--upstreampad",
type="int",
default=100,
dest="upstream",
help="upstream")
parser.add_option("--downstreampad",
type="int",
default=100,
dest="downstream",
help="downstream")
parser.add_option("--ref",
type="string",
default="human_reference_v37.fa",
dest="ref",
help="name of reference assembly (fasta) file (.fa)")
parser.add_option("--bamprefix",
type="string",
default=None,
dest="bamprefix",
help="output prefix of bam file")
(options, args) = parser.parse_args()
if options.bamprefix == None:
sys.write("please provide a value to --bamprefix option!\n ")
sys.exit(1)
bamfile = args[0]
if os.path.isfile(bamfile) == False:
sys.stderr.write("bam file doesn't exists! " + bamfile + "\n")
sys.exit(1)
bamindexfile = bamfile + ".bai"
if os.path.isfile(bamindexfile) == False:
sys.stderr.write(
"bam index file doesn't exist! did you run samtools/bamtools index?\n"
)
sys.exit(1)
if os.path.isfile(options.bedfile) == False:
sys.stderr.write("bed file doesn't exist! " + options.bedfile + "\n")
exit(1)
bam = pysam.Samfile(bamfile, "rb")
bedfh = open(options.bedfile, 'r')
for coord_tuple in yield_bedcoordinate(bedfh):
(chr, start, end) = coord_tuple
regionstring = chr + ":" + start + ".." + end
regionstring = ":".join([
chr,
str(int(start) - options.upstream),
str(int(end) + options.downstream)
])
bamfilename = ".".join([options.bamprefix, regionstring, 'bam'])
#now create a bamfile for the region defined by the bed coordinate, plus/minus the pad
#the bamfile is names as bamfileprefix.regionstring.bam
outbam = pysam.Samfile(bamfilename, "wb", template=bam)
print coord_tuple
print chr, str(int(start) -
options.upstream), str(int(end) + options.downstream)
#now for each aligned read in the region, write it to the bam file
for alignedread in bam.fetch(chr,
int(start) - options.upstream,
int(end) + options.downstream):
if alignedread.is_paired:
outbam.write(alignedread)
outbam.close()
bam.close()
""" brace_close : RBRACE
"""
self._pop_scope()
p[0] = p[1]
def p_empty(self, p):
'empty : '
p[0] = None
def p_error(self, p):
if p:
self._parse_error('before: %s' % p.value, self._coord(p.lineno))
else:
self._parse_error('At end of input', '')
if __name__ == "__main__":
import pprint
import time, sys
t1 = time.time()
parser = CParser(lex_optimize=True, yacc_debug=True, yacc_optimize=False)
sys.write(time.time() - t1)
buf = '''
int (*k)(int);
'''
# set debuglevel to 2 for debugging
t = parser.parse(buf, 'x.c', debuglevel=0)
t.show(showcoord=True)
def errfoo(msg, a, b):
sys.write(msg + "\n")
sys.exit()
def shell(parenthed):
global namespace
command = parenthed[0]
argv = parenthed[1:]
if command == "+" and len(argv) == 1:
return argv[0]
elif command == "+" and len(argv) == 2:
return str(int(argv[0])+int(argv[1]))
elif command == "-" and len(argv) == 1:
return str(-int(argv[0]))
elif command == "-" and len(argv) == 2:
return str(int(argv[0])-int(argv[1]))
elif command == "*" and len(argv) == 1:
return namespace[argv[0]]
elif command == "*" and len(argv) == 2:
return str(int(argv[0])*int(arg[0]))
elif command == "/" and len(argv) == 2:
return str(int(int(argv[0])/int(argv[0])))
elif command == "%" and len(argv) == 1:
return str(abs(int(argv[0])))
elif command == "%" and len(argv) == 2:
return str(int(argv[0])%int(argv[1]))
elif command == "=" and len(argv) == 2:
return str(int(argv[0]==argv[1]))
elif command == "!=" and len(argv) == 2:
return str(int(argv[0]!=argv[1]))
elif command == ">" and len(argv) == 2:
return str(int(int(argv[0])>int(argv[1])))
elif command == ">=" and len(argv) == 2:
return str(int(int(argv[0])>=int(argv[1])))
elif command == "<" and len(argv) == 2:
return str(int(int(argv[0])<int(argv[1])))
elif command == "<=" and len(argv) == 2:
return str(int(int(argv[0])<=int(argv[1])))
elif command == "&" and len(argv) == 2:
return str(int(argv[0])&int(argv[1]))
elif command == "|" and len(argv) == 2:
return str(int(argv[0])|int(argv[1]))
elif command == "^" and len(argv) == 2:
return str(int(argv[0])^int(argv[1]))
elif command == "!" and len(argv) == 1:
return str(int(not bool(int(argv[0]))))
elif command == "~" and len(argv) == 1:
return str(~int(argv[0]))
elif command == "~" and len(argv) == 2:
return argv[0]+argv[1]
elif command == ":=" and len(argv) == 2:
s = argv[1]
namespace[argv[0]] = argv[1]
return s
elif command == "'" and len(argv) == 1:
return chr(int(argv[0]))
elif command == "@" and len(argv) == 1:
return str(ord(argv[0]))
elif command == "@" and len(argv) == 2:
return argv[0].split("`")[int(argv[1])]
elif command == "?" and len(argv) == 3:
if bool(int(argv[0])):
return argv[1]
else:
return argv[2]
elif command == "if" and len(argv) == 2:
if bool(int(argv[0])):
return run(argv[1])
elif command == "ifelse" and len(argv) == 3:
if bool(int(argv[0])):
return run(argv[1])
else:
return run(argv[2])
elif command == "while" and len(argv) == 2:
while True:
s = run(argv[0])
t = run(argv[1])
if bool(int(s)):
return t
elif command == "do" and len(argv) == 1:
return run(argv[0])
elif command == "write" and len(argv) == 1:
import sys
sys.write(argv[0])
return ""
elif command == "writeln" and len(argv) == 1:
print(argv[0])
return ""
elif command == " ":
return "`".join(argv)
elif command == "@:=" and len(argv) == 3:
s = argv[0].split("`")
s[int(argv[1])] = argv[2]
return "`".join(s)
elif command == "~~" and len(argv) == 2:
return argv[0]+"`"+argv[1]
elif command == "exit" and len(argv) == 0:
import sys
sys.exit()
elif command == "#" and len(argv) == 1:
return len(argv[0])
elif command == "##" and len(argv) == 1:
return len(argv[0].split("`"))
elif command == "]" and len(argv) == 2:
s = open(argv[1],"w")
s.write(argv[0]+"\n")
s.close()
return argv[0]+"\n"
elif command == "]." and len(argv) == 2:
s = open(argv[1],"w")
s.write(argv[0])
s.close()
return argv[0]
elif command == "[" and len(argv) == 1:
s = open(argv[0],"r")
txt = s.read()
s.close()
return txt
elif command == "]]" and len(argv) == 2:
s = open(argv[1],"a")
s.write(argv[0]+"\n")
s.close()
return argv[0]+"\n"
elif command == "]]." and len(argv) == 2:
s = open(argv[1],"a")
s.write(argv[0])
s.close()
return argv[0]
elif command == "cd" and len(argv) == 0:
import os
return os.getcwd()
elif command == "cd" and len(argv) == 1:
import os
os.chdir(argv[0])
return os.getcwd()
elif command == "ls":
import os
return '`'.join(os.listdir(os.getcwd()))
elif command == "readln":
try:
return raw_input()
except:
return input()
def my_error_func(msg, a, b):
sys.write(msg + "\n")
sys.exit()
args.add_argument('builddir', nargs = '?', default = '.')
args.add_argument('--cxxflags', default = '')
args.add_argument('--debug', action = 'store_true')
args.add_argument('--testpath', help = 'PATH containing llvm-lit and FileCheck')
args.add_argument('--withtests', action = 'store_true')
args = args.parse_args()
bootstrap = os.path.realpath(sys.argv[0])
builddir = os.path.realpath(args.builddir)
if not os.path.exists(builddir):
os.makedirs(builddir)
if not os.path.isdir(builddir):
sys.write("Build directory '%s' is not a directory" % args.builddir)
sys.exit(1)
# First, let's declare what we actually want to build.
cxx_srcs = {
'bin/': (
'CLIArguments',
'fab',
),
'lib/': (
'AssertionFailure', 'Bytestream', 'ErrorReport', 'Fabrique', 'FabBuilder',
'Printable', 'SemanticException',
'SourceCodeException', 'SourceLocation', 'SourceRange', 'UserError',
'builtins', 'names', 'strings',
),
"""
Wrapper that execute a program and its arguments but reports standard error
messages only if the program exit status was not 0
Example: ./stderr_wrapper.py myprog arg1 -f arg2
"""
import sys, subprocess, os
assert sys.version_info[:2] >= ( 2, 4 )
TRINITY_BASE_DIR = ""
if os.environ.has_key('TRINITY_HOME'):
TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
else:
sys.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
sys.stderr.write("You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this");
sys.exit(1)
# get bindir
bindir = sys.argv[0]
bindir = bindir.split("/")
if len(bindir) > 1:
bindir.pop()
bindir = "/".join(bindir)
else:
bindir = "."
def errfoo(msg, a, b):
sys.write(msg + '\n')
sys.exit()
def errfoo(msg, a, b):
sys.write(msg + "\n")
sys.exit()
def classify(train_list, test_list, parent_dir):
index_list = {}
# initialize matrix
matrix = output.Matrix(map_list.index.keys())
for i, c in enumerate(map_list.index.keys()):
subdir = str(i + 1) + '-vs-all/'
dir = parent_dir + subdir
#check if sub directory already exists
if not os.path.exists(dir):
os.makedirs(dir)
train = open(dir + 'train', 'w')
index_list[i + 1] = c
mapf.write("%s %d\n" % (c, i + 1))
for t in train_list:
if re.search(c, t.cls):
gold_class = 1
else:
gold_class = -1
train.write("%s %d %s\n" % (t.instance, gold_class, t.features))
train.close()
test = open(dir + 'test', 'w')
for t in test_list:
if re.search(c, t.cls):
gold_class = 1
else:
gold_class = -1
test.write("%s %d %s\n" % (t.instance, gold_class, t.features))
test.close()
#run train.txt
call_mallet(dir)
#create sys_output from test.stdout
temp = open(dir + 'stdout', 'r')
sys = open(dir + 'sys_output', 'w')
for l in temp.readlines():
m = re.match('^(\S+) (\-?\d) (\-?\d):(\S+) (\-?\d):(\S+)', l)
if m:
sys.write("%s %s %s %s %s %s\n" % \
(m.group(1),m.group(2),m.group(3),m.group(4),m.group(5),m.group(6)))
#store test probability into each table
for t in test_list:
if t.instance == m.group(1):
if m.group(3) != '-1':
prob = m.group(4)
else:
prob = m.group(6)
t.probs[i + 1] = prob
temp.close()
sys.close()
#assign class with highest probability
for t in test_list:
final = sorted(t.probs.items(),
key=lambda x: float(x[1]),
reverse=True)
index = final[0][0]
sys_class = index_list[index]
matrix.set_value(t.cls, sys_class, 1)
#output
final_sys.write("%s %s" % (t.instance, t.cls))
for cls, prob in final:
final_sys.write(" %s %s" % (index_list[cls], prob))
final_sys.write('\n')
return matrix
import sys
filename = input("enter filename:")
fp = open(filename, "w")
ch = input("enter string:")
while ch != '#':
fp.write(ch)
sys.write(ch)
ch = input()
fp.close()
# finally check if dispersion is sane before proceeding
currentDispersion = wallClockClient.algorithm.getCurrentDispersion()
if currentDispersion > 1000000000*1.0:
sys.stderr.write("\n\nWall clock client synced with dispersion +/- %f.3 milliseconds." % (currentDispersion / 1000000.0))
sys.stderr.write("\nWhich is greater than +/- 1 second. Aborting.\n\n")
sys.exit(1)
print
print "Beginning to measure"
measurer.capture()
# sanity check we are still connected to the CSS-TS server
if not syncTimelineClockController.connected and syncTimelineClockController.timelineAvailable:
sys.write("\n\nLost connection to CSS-TS or timeline became unavailable. Aborting.\n\n")
sys.exit(1)
measurer.detectBeepsAndFlashes(dispersionFunc = dispRecorder.dispersionAt)
for channel in measurer.getComparisonChannels():
try:
index, expected, timeDifferencesAndErrors = measurer.doComparison(channel)
print
print "Results for channel: %s" % channel["pinName"]
print "----------------------------"
stats.calcAndPrintStats(index, expected, timeDifferencesAndErrors, cmdParser.args.toleranceSecs[0])
except DubiousInput:
def my_error_func(msg, a, b):
sys.write(msg + "\n")
sys.exit()
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
###############################################################################
#
# $Id: regress.py.in,v 1.1 2004/07/31 00:58:05 rivetwa Exp $
#
# # regress/regress.py. Generated from regress.py.in by configure.
import os, os.path, sys, fnmatch, glob
# Check the python version
_v = sys.version_info
_ver = (int(_v[0]) << 16) + (int(_v[1]) << 8) + int(_v[2])
if _ver < 0x020101:
sys.write('You need python >= 2.1.1 to run this program.\n')
sys.write('Your python version is:\n%s\n' %(sys.version))
sys.exit(1)
# Add modules dir to module search path
sys.path.append('modules')
import base_test
"""Main regression test driver program.
Test cases are organised into three levels: directories -> modules -> classes.
Directories are the most generic and classes are the most specific.
This program will search the current directory for subdirectories with names
matching 'test_*'. Each matching subdirectory will be searched for python
def lexerErrorFunc(self, msg, a, b):
sys.write(msg + '\n')
sys.exit()
import csv
import sys
import math
if len(sys.argv) < 2:
sys.write("Usage: " + sys.argv[0] + " #column\n")
sys.exit(-1)
column = int(sys.argv[1])
fd = sys.stdin
csv_reader = csv.reader(fd, delimiter=',')
previous_value = 0
previous_time = 0
for row in csv_reader:
start_sec = float(row[0])
start_nsec = float(row[1])
time = start_sec + (start_nsec * math.pow(10,-9))
value = float(row[column])
diff = (value - previous_value)/(time - previous_time)
diff_str = str(diff)
row.append(diff_str)
output_str = ",".join(row)
sys.stdout.write(output_str + "\n")
#Update history
previous_time = time
previous_value = value
import itertools, sys
lambda n: sys.write( itertools.takewhile(lambda n: n != 1, itertools.imap(lambda n_ptr: n_ptr[0] = n_ptr[0]/2.0 if n_ptr[0]%2 == 0 else 3*n_ptr[0]+1, [n])))
collatz = lambda n_ptr:
n_ptr[0] = n_ptr[0]/2.0 if n_ptr[0]%2 == 0 else 3*n_ptr[0]+1
lambda n: map(lambda n_ptr: n_ptr[0]/2.0 if n_ptr[0]%2 == 0 else 3*n_ptr[0]+1, [])
while(collatz([n]) != 1)
def docollatz(n):
yield n
Xraise StopIteration
sys.
for j in xrange(len(img[i])):
if img[i][j] < th: img2[i][j] = 255
else: img2[i][j] = img[i][j]
return img2
tjreq = requests.Session()
tjresp1 = tjreq.get(tjurl + search_path)
tjresp2 = tjreq.get(tjurl + processo_path)
#print tjresp.text
html_page1 = bs.BeautifulSoup(tjresp1.text.encode('latin1'))
html_page2 = bs.BeautifulSoup(tjresp2.text.encode('latin1'))
counter = 1
while not html_page1.find(text=n_processo) or not html_page2.find(text=n_processo):
sys.write('attempts: {0}\r'.format(counter))
counter += 1
tjresp1 = tjreq.get(tjurl + search_path)
tjresp2 = tjreq.get(tjurl + processo_path)
html_page1 = bs.BeautifulSoup(tjresp1.text.encode('latin1'))
html_page2 = bs.BeautifulSoup(tjresp2.text.encode('latin1'))
#process = html_page.find(text=n_processo)
#with open(process + '.html','w') as fp: fp.write( tjresp.text.encode('latin1'))
print 'founded after {0} attempts!'.format(counter)
process = requests.get(tjurl + processo_path)
outfile = 'movimentacao-' + now() + n_processo + '.html'
with open(outfile,'w') as fp: fp.write( process.text.encode('latin1') )
print 'printed in {0} after {1} attempts'.format(outfile,counter)
# finally check if dispersion is sane before proceeding
currentDispersion = wallClockClient.algorithm.getCurrentDispersion()
if currentDispersion > 1000000000*1.0:
sys.stderr.write("\n\nWall clock client synced with dispersion +/- %f.3 milliseconds." % (currentDispersion / 1000000.0))
sys.stderr.write("\nWhich is greater than +/- 1 second. Aborting.\n\n")
sys.exit(1)
print
print "Beginning to measure"
measurer.capture()
# sanity check we are still connected to the CSS-TS server
if not syncTimelineClockController.connected and syncTimelineClockController.timelineAvailable:
sys.write("\n\nLost connection to CSS-TS or timeline became unavailable. Aborting.\n\n")
sys.exit(1)
measurer.detectBeepsAndFlashes(dispersionFunc = dispRecorder.dispersionAt)
for channel in measurer.getComparisonChannels():
try:
index, expected, timeDifferencesAndErrors = measurer.doComparison(channel)
print
print "Results for channel: %s" % channel["pinName"]
print "----------------------------"
stats.calcAndPrintStats(index, expected, timeDifferencesAndErrors, cmdParser.args.toleranceSecs[0])
except DubiousInput:
def main():
# Parse CL
elements_needed = int(5)
args_array = np.array(sys.argv)
N_args = len(args_array)
assert(N_args == elements_needed)
N_jackknife = int(args_array[1])
todo_dir = args_array[2]
file_dir = args_array[3]
out_dir = args_array[4]
if not(os.path.isdir(out_dir)):
sys.stderr.write('{} does not exist. Making...\n'.format(out_dir))
cmd='mkdir ' + out_dir
os.system(cmd)
# load the todo pointing list
input_filename = todo_dir + 'todo_list.dat'
if not(os.path.isfile(input_filename)):
sys.write('Error: {} does not exist. Exiting...\n'.format(input_filename))
sys.exit()
sys.stderr.write('Loading pointing info from file {} ...\n'.format(input_filename))
input_file = open(input_filename, 'rb')
todo_list = pickle.load(input_file)
input_file.close()
sys.stderr.write('Jackknifing uniform from {}\n'.format(file_dir))
for p in todo_list:
# Uniform files are random upon creation so no need to shuffle
filename = file_dir + 'uniform_' + p.ID + '.xyzw.dat'
if not(os.path.isfile(filename)):
sys.write('Error: {} does not exist. Exiting...\n'.format(filename))
sys.exit()
xyzw = np.genfromtxt( filename, skip_header=1 )
# jackknife samples
N_uni = len( xyzw )
remain = N_uni % N_jackknife
for i in range( N_jackknife ):
# Make every sub-sample the same size
slice_length = int(N_uni / N_jackknife)
lower_ind = i * slice_length
upper_ind = lower_ind + slice_length
remove_me = np.arange(lower_ind, upper_ind, 1)
# Remove slice
xyzw_temp = np.delete(xyzw, remove_me, 0)
N_temp = len(xyzw_temp)
# Output jackknife'd file
out_file = out_dir + 'uniform_' + p.ID + '_jk_' + str(i) + '.dat'
np.savetxt(out_file, xyzw_temp, fmt='%1.6f')
# Add number of elements as first line in file
line_prepender(out_file, str(N_temp))
sys.stderr.write('Jackknife sample output to {} . \n\n'.format(out_dir))
"""Serializers"""
import sys
try:
import json
except ImportError:
try:
import simplejson as json
except ImportError:
sys.write('ERROR: Please install the `json` or `simplejson` module')
sys.exit(-1)
class JsonSerializer(object):
"""Simple JSON serializer"""
def encode(self, data):
return json.dumps(data)
def decode(self, data):
return json.loads(data)
p[0] = p[1]
def p_empty(self, p):
'empty : '
p[0] = None
def p_error(self, p):
if p:
self._parse_error(
'before: %s' % p.value,
self._coord(p.lineno))
else:
self._parse_error('At end of input', '')
if __name__ == "__main__":
import pprint
import time, sys
t1 = time.time()
parser = CParser(lex_optimize=True, yacc_debug=True, yacc_optimize=False)
sys.write(time.time() - t1)
buf = '''
int (*k)(int);
'''
# set debuglevel to 2 for debugging
t = parser.parse(buf, 'x.c', debuglevel=0)
t.show(showcoord=True)
def classify(train_list,test_list,parent_dir):
index_list = {}
# initialize matrix
matrix = output.Matrix(map_list.index.keys())
for i,c in enumerate(map_list.index.keys()):
subdir = str(i+1) + '-vs-all/'
dir = parent_dir + subdir
#check if sub directory already exists
if not os.path.exists(dir):
os.makedirs(dir)
train = open(dir + 'train','w')
index_list[i+1] = c
mapf.write("%s %d\n" % (c,i+1))
for t in train_list:
if re.search(c,t.cls):
gold_class = 1
else:
gold_class = -1
train.write("%s %d %s\n" % (t.instance,gold_class,t.features))
train.close()
test = open(dir + 'test','w')
for t in test_list:
if re.search(c,t.cls):
gold_class = 1
else:
gold_class = -1
test.write("%s %d %s\n" % (t.instance,gold_class,t.features))
test.close()
#run train.txt
call_mallet(dir)
#create sys_output from test.stdout
temp = open(dir + 'stdout','r')
sys = open(dir + 'sys_output','w')
for l in temp.readlines():
m = re.match('^(\S+) (\-?\d) (\-?\d):(\S+) (\-?\d):(\S+)',l)
if m:
sys.write("%s %s %s %s %s %s\n" % \
(m.group(1),m.group(2),m.group(3),m.group(4),m.group(5),m.group(6)))
#store test probability into each table
for t in test_list:
if t.instance == m.group(1):
if m.group(3) != '-1':
prob = m.group(4)
else:
prob = m.group(6)
t.probs[i+1] = prob
temp.close()
sys.close()
#assign class with highest probability
for t in test_list:
final = sorted(t.probs.items(),key=lambda x:float(x[1]),reverse=True)
index = final[0][0]
sys_class = index_list[index]
matrix.set_value(t.cls,sys_class,1)
#output
final_sys.write("%s %s" %(t.instance,t.cls))
for cls,prob in final:
final_sys.write(" %s %s" %(index_list[cls],prob))
final_sys.write('\n')
return matrix
parser.add_argument('-o','--outfile', type=argparse.FileType('w'), help ="MSA output file", required=True)
parser.add_argument('-v','--outformat', default="clustal", help ="MSA output format")
parser.add_argument('-l','--list', type=argparse.FileType('r'), required = True)
args = parser.parse_args()
sel_seqs = args.list.read().split()
msa_data = AlignIO.read(args.msa_file, args.informat)
sel_align = []
found_align = []
for align in msa_data:
if align.id in sel_seqs:
sel_align.append(align)
found_align.append(align.id)
AlignIO.write(AlignIO.MultipleSeqAlignment(sel_align), args.outfile, args.outformat)
[ sys.write("Not found:\t{}".format(align.id)) for seq_id in found_align if seq_id not in found_align ]
"""Serializers"""
import sys
try:
import json
except ImportError:
try:
import simplejson as json
except ImportError:
sys.write('ERROR: Please install the `json` or `simplejson` module')
sys.exit(-1)
class JsonSerializer(object):
"""Simple JSON serializer"""
def encode(self, data):
return json.dumps(data)
def decode(self, data):
return json.loads(data)
def main():
# Parse CL
elements_needed = int(6)
args_array = np.array(sys.argv)
N_args = len(args_array)
assert (N_args == elements_needed)
N_jackknife = int(args_array[1])
todo_dir = args_array[2]
bins_dir = args_array[3]
jk_dir = args_array[4]
out_dir = args_array[5]
if not (os.path.isdir(out_dir)):
sys.stderr.write('{} does not exist. Making...\n'.format(out_dir))
cmd = 'mkdir ' + out_dir
os.system(cmd)
# load the todo pointing list
input_filename = todo_dir + 'todo_list.dat'
if not (os.path.isfile(input_filename)):
sys.write(
'Error: {} does not exist. Exiting...\n'.format(input_filename))
sys.exit()
sys.stderr.write(
'Loading pointing info from file {} ...\n'.format(input_filename))
input_file = open(input_filename, 'rb')
todo_list = pickle.load(input_file)
input_file.close()
# load bin settings
bins_filename = bins_dir + 'rbins.ascii.dat'
if not os.path.isfile(bins_filename):
sys.stderr.write(
'Error: {} does not exist. Exiting...\n'.format(bins_filename))
sys.exit()
bins = np.genfromtxt(bins_filename, skip_header=1)
N_rbins = len(bins)
cleaned_dir = mwu.get_path.get_cleandata_path()
scripts_dir = mwu.get_path.get_scripts_path()
pairs_dir = scripts_dir + 'pair_count/'
exe_dir = './bin/'
# Check for dir/file existence
if not os.path.isdir(exe_dir):
sys.stderr.write(
'{} does not exist Making directory...\n'.format(exe_dir))
cmd = 'mkdir ' + exe_dir
os.system(cmd)
pairs_file = exe_dir + 'pair_count'
if not os.path.isfile(pairs_file):
sys.stderr.write(
'{} does not exist. Compiling...\n'.format(pairs_file))
# find system and use either icc or gcc
current_sys = mwu.get_path.get_system()
if current_sys == 'bender':
cmd = 'bash ' + pairs_dir + 'icc_compile_pair_count.sh ' + pairs_dir
elif current_sys == 'Adams-MacBook-Pro-2':
cmd = 'bash ' + pairs_dir + 'gcc_compile_pair_count.sh ' + pairs_dir
else:
raise ValueError('Unrecognized system...\n')
os.system(cmd)
else:
sys.stderr.write('Using already compiled file {}'.format(pairs_file))
# Main loop
for p in todo_list:
# Make array to store raw dd counts for different jackknife samples
counts_jk = np.zeros((N_jackknife, N_rbins))
# Each file will have the exact same norm b/c same N
norm = np.zeros(N_rbins)
# counting pairs for each jackknife sample and load pairs into array
for i in range(N_jackknife):
jackknife_filename = jk_dir + 'mock_' + p.ID + '_jk_' + str(
i) + '.dat'
counts_filename = jk_dir + 'mock_' + p.ID + '_jk_' + str(
i) + '.ddcounts.dat'
cmd = (pairs_file + ' ' + jackknife_filename + ' ' +
bins_filename + ' > ' + counts_filename)
os.system(cmd)
counts_jk[i, :], norm = np.genfromtxt(counts_filename,
unpack=True,
usecols=[5, 6])
jk_mean = np.mean(counts_jk, axis=0)
jk_std = np.std(counts_jk, axis=0) * np.sqrt(N_jackknife - 1)
# Normalize counts
jk_mean /= norm
jk_std /= norm
jk_data = np.column_stack((jk_mean, jk_std))
tol = 1e-8
jk_frac = np.zeros(len(jk_mean))
for i in range(len(jk_frac)):
if (jk_mean[i] > tol):
jk_frac[i] = jk_std[i] / jk_mean[i]
output_filename = jk_dir + 'mean_std_' + p.ID + '.dat'
np.savetxt(output_filename, jk_data, fmt='%1.6e')
frac_filename = jk_dir + 'frac_err_jk_DD_' + p.ID + '.dat'
np.savetxt(frac_filename, jk_frac, fmt='%1.6e')
def generate_bed_line(sam):
if sam[:1] == "@":
return
for i in range(len(sam)):
if sam[i].startswith("NM:"):
# NM stores the edit distance between read and ref
sam_index_space_pos = i
elif sam[i].startswith("MD:"):
# MD stores the string for mismatching positions
sam_mismatches_pos = i
elif sam[i].startswith("NH:"):
# store number of mappings for that read
read_weight = 1.0 / float(sam[i].replace("NH:i:", ""))
# CONSTANTS
BED_CHR = 0
BED_START = 1
BED_STOP = 2
BED_READ = 3
BED_SCORE = 4
BED_STRAND = 5
BED_MID = 6
SAM_READ_ID = 0
SAM_FLAG = 1
SAM_CHR = 2
SAM_START = 3
SAM_SCORE = 4
SAM_MID = 5 # aka cigar string
SAM_STAR = 6 # next entry on same chromosome?
SAM__ = 7 # mate info
SAM__ = 8 # mate info
SAM_READ = 9
SAM_STAR = 10
SAM__ = 42
SAM_INDEX_SPACE = sam_index_space_pos
SAM_MISMATCHES = sam_mismatches_pos
# 5th digit in SAM_FLAG in binary format tells the strand: 0 -> plus, 1 -> minus
#Now reading in the sam_tuples sequentially.
#Need to convert this in some kind of bed format
MID_length = get_match_length(sam[SAM_MID])
strand = "?"
SAM_FLAG_BINARY = '{0:012b}'.format(int(sam[SAM_FLAG]))
SAM_STRAND = int(SAM_FLAG_BINARY[::-1][4])
if SAM_STRAND == 0:
strand = "+"
elif SAM_STRAND == 1:
strand = "-"
else:
sys.write("[ERROR] Could not infer strand from " + SAM_FLAG + "\n")
sys.exit(2)
bed_line = ""
bed_line += sam[SAM_CHR] + "\t"
bed_line += str(int(sam[SAM_START]) - 1) + "\t"
bed_line += str(int(sam[SAM_START]) - 1 + MID_length) + "\t"
bed_line += sam[SAM_READ_ID] + "\t"
# the read weight is later on overwritten by the edit distance
bed_line += str(read_weight) + "\t"
bed_line += strand
#At this point, the bed file is almost complete, just needs the MMID
#Make a tuple with it!
bed = bed_line.split("\t")
g_length = MID_length
# genome is set as only "?" because we don't know the seqeuence
g = "".ljust(g_length, "?")
g = list(g)
# get the read that was aligned
soft_clipped_start = 0
soft_clipped_end = 0
match_splitted = re.split(r'(\d+)', sam[SAM_MID])
match_splitted.pop(0) # re produces a weird '' as elem 0 ...
if match_splitted[1] == "S":
soft_clipped_start = match_splitted[0]
if match_splitted[-1] == "S":
soft_clipped_end = match_splitted[-2]
# take only the portion of the read that was aligned to the reference
# (i.e. omit soft clippings at the start and at the end)
last_pos = len(sam[SAM_READ]) - int(soft_clipped_end)
r = sam[SAM_READ][int(soft_clipped_start):last_pos]
r = list(r)
# save the final reference and read sequences
G = []
R = []
current_MID = sam[SAM_MID]
exploded_MID = re.split(r'(\d+|[A-Za-z])', current_MID)
for item in exploded_MID:
if item == '':
exploded_MID.remove(item)
### Do alignment read vs genome
for i in range(int(len(exploded_MID) / 2)):
number = int(exploded_MID[i * 2])
type = exploded_MID[i * 2 + 1]
# no need to process type "N" at this point
# because currently the genomic seq anyways
# only consists of "?"
if type == "M":
# read and reference were aligned
for _ in itertools.repeat(None, number):
G.append(g.pop(0))
R.append(r.pop(0))
elif type == "I":
# nucleotides in read that are not there in the reference
for _ in itertools.repeat(None, number):
G.append("-")
R.append(r.pop(0))
elif type == "D":
# nucleotides in reference that are not there in the read
for _ in itertools.repeat(None, number):
G.append(g.pop(0))
R.append("-")
mismatch = sam[SAM_MISMATCHES]
mismatch = mismatch.split(":")[-1]
mismatch = mismatch.replace("^", "")
mismatch_splitted = re.split(r'(\d+|[A-Za-z])', mismatch)
for item in mismatch_splitted:
if item == '':
mismatch_splitted.remove(item)
pointer = 0
for c in mismatch_splitted:
if c == '':
continue # Skip c and this iteration when this happens
# Skip the next G[pointer] that is not a dash
if c.isdigit():
# perfect match here
value = int(c)
while value > 0:
# skip gaps in the reference because insertions are
# not present in the mismatch string
if G[pointer] == '-':
pointer += 1
else:
# go over a region of perfect matches
pointer += 1
value -= 1
else:
# again
# skip gaps in the reference because insertions
# are not present in the mismatch string
while G[pointer] == '-':
pointer += 1
# exchange question mark in the reference
# two possible reasons:
# 1. mismatch; 2. deletion
G.pop(pointer)
G.insert(pointer, c)
pointer += 1
# for the MMID, track the positions of the mismatches and deletions
# final MMID looks like:
# 15MATIGDCDT12 (15 matches -> 1 Mismatch( A ref, T in read) -> 1 insertion (G in read) -> 1 deletion (C in reference) -> 1 deletion (T in reference) -> 12 matches
match_count = 0
MMID = ""
g_index = 0
r_index = 0
for index in range(len(G)):
cg = G[index]
cr = R[index]
if cg == "?":
match_count += 1
else:
if match_count > 0:
MMID += str(match_count)
match_count = 0
if cg == "-":
MMID += "I" + cr
elif cr == "-":
MMID += "D" + cg
else:
MMID += "M" + cg + cr
# note by RS 2016-06-01: this increment statement
# should not effect the loop as far as I understood python
# (was introduced not by me but by Manuel)
index += 1
if match_count > 0:
MMID += str(match_count)
match_count = 0
index_space = sam[SAM_INDEX_SPACE]
index_space = index_space.split(":")[-1]
new_bed = list(bed)
# exchange read weight by edit distance and
# define the read weight later on
new_bed.pop(4)
new_bed.insert(4, index_space)
new_bed.append(MMID)
new_file_line = "\t".join(new_bed)
return new_file_line
"""
Wrapper that execute a program and its arguments but reports standard error
messages only if the program exit status was not 0
Example: ./stderr_wrapper.py myprog arg1 -f arg2
"""
import sys, subprocess, os
assert sys.version_info[:2] >= (2, 4)
TRINITY_BASE_DIR = ""
if os.environ.has_key('TRINITY_HOME'):
TRINITY_BASE_DIR = os.environ['TRINITY_HOME']
else:
sys.write(
"You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this"
)
sys.stderr.write(
"You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this"
)
sys.exit(1)
# get bindir
bindir = sys.argv[0]
bindir = bindir.split("/")
if len(bindir) > 1:
bindir.pop()
bindir = "/".join(bindir)
else:
bindir = "."
#
#
# This little script offers decryption and verification of the existing
# Ethereum wallets, as well as generation of a new wallet. You can use any
# utf-8 string as the password, which could provide with better security
# against the brute-force attack.
# Use at your own risk.
#
# Example:
# python3 ./keytree.py
import os
import sys
if sys.version_info[1] < 7:
sys.write("Python should be >= 3.7")
sys.exit(1)
basedir = os.path.dirname(os.path.abspath(__file__))
sys.path.insert(0, basedir + "/frozen_deps")
import re
import argparse
import hashlib
import hmac
import unicodedata
import json
from getpass import getpass as _getpass
import bech32
import mnemonic
from ecdsa import SigningKey, VerifyingKey, SECP256k1
def run(self):
self.out = sys.stdout
self.data = []
re_linemarker = re.compile(r"^# (\d+) \"(.+)\"$")
re_mnemonic = re.compile("^//\s+MNEMONIC:\s+")
re_start = re.compile("^\s*start\s+")
try:
if self.args.filename is None:
f = sys.stdin
self.fname = self.args.filename
else:
f = open(self.args.filename)
self.fname = '<stdin>'
# comment_queue = []
# uprogram_queue = []
# obj = OrderedDict()
block = []
self.linenum = 0
state = 0
for line in f:
line = line.strip()
self.linenum += 1
if self.args.verbose:
print(state, line)
# Is this a preprocessor linemarker?
m = re_linemarker.match(line)
if m:
linenum, fname = m.groups()
linenum = int(linenum)
if state == 0 and re_mnemonic.match(line):
state = 1
if block:
self.process(block)
block = [line]
continue
if state == 1:
block.append(line)
if re_start.match(line):
state = 2
continue
if state == 2:
if re_mnemonic.match(line):
state = 1
if block:
self.process(block)
block = [line]
continue
else:
block.append(line)
continue
# At the end, process any remaining blocks, provided we've seen
# documentation comments and micoprograms (state 2).
if state == 2 and block:
self.process(block)
except BrokenPipeError:
sys.write("Broken pipe\n")
sys.exit(1)
self.report()
from xlrd import open_workbook
import argparse
import sys
parser = argparse.ArgumentParser()
parser.add_argument("-f", "--file", dest="inputFile", required=True)
args = parser.parse_args()
wb = open_workbook(args.inputFile)
s = wb.sheets()[0]
for row in range(s.nrows):
values = []
for col in range(s.ncols):
values.append(s.cell(row,col).value)
sys.write("\t".join(values))
#!/usr/bin/python3.4
import time
import sys
for i in range(5):
# print('\r' ,i)
sys.write(1,bytes(format(i,:qw)))
sys.stdout.flush()
time.sleep(1)