def get_info(cls):
'''Implements ISynthesizer.get_info.'''
if cls.INFO is None:
out = iterpipes.run(iterpipes.linecmd('speak --voices'))
# get voices from fixed width columns
voices = [ln[40:52].strip() for i, ln in enumerate(out) if i > 0]
# generate all variants for voices
variants = ['', '+f1', '+f2', '+f3', '+f4', '+m1', '+m2', '+m3',
'+m4', '+m5', '+m6', '+whisper', '+croak']
voices = itertools.chain(*[
[voice+variant for voice in voices]
for variant in variants
])
cls.INFO = {
'rate' : {
'minimum' : cls.MIN_RATE,
'maximum' : cls.MAX_RATE,
'default' : 200
},
'pitch' : {
'minimum' : 0.0,
'maximum' : 1.0,
'default' : 0.5
},
'voices' : {
'values' : list(voices),
'default' : 'default'
}
}
return cls.INFO
def runIgBlastp( query, germlineSpecie = GERMLINE_HUMAN, domainSystem = DOMAIN_IMGT,
additionalDB = None, numThreads = 4, numAlignments = 10, outfmt = 3, out = None ):
igblastp = os.path.join(os.path.join('.', IGBLAST_BIN), "igblastp")
params = []
if query == "" or germlineSpecie == "" or domainSystem not in [DOMAIN_IMGT, DOMAIN_KABAT]:
return None
# Query
query = os.path.abspath(query)
igblastp += " -query {}"
params.append(query)
# Germline
germlineSpecie = "{0}/{1}_gl_V".format(IGBLAST_GERMLINE, germlineSpecie)
igblastp += " -germline_db_V {}"
params.append(germlineSpecie)
# Domain
igblastp += " -domain_system {}"
params.append(domainSystem)
# Database
if additionalDB != None:
additionalDB = os.path.join(BLASTDB_PATH, additionalDB)
igblastp += " -db {}"
params.append(additionalDB)
# Threads
igblastp += " -num_threads {}"
params.append(str(numThreads))
# Alignments
igblastp += " -num_alignments {}"
params.append(str(numAlignments))
# Output format
igblastp += " -outfmt {}"
params.append(str(outfmt))
# Output file
if out != None:
igblastp += " -out {}"
params.append(out)
# RUN IGBLASTP
cur = os.path.curdir
os.chdir(IGBLAST_PATH)
runLine = iterpipes.linecmd(igblastp, *params)
result = iterpipes.run(runLine)
os.chdir(cur)
returnResult = ""
for line in result:
returnResult += line
return returnResult
def get_info(cls):
"""Implements ISynthesizer.get_info."""
if cls.INFO is None:
out = iterpipes.run(iterpipes.linecmd("speak --voices"))
# get voices from fixed width columns
voices = [ln[40:52].strip() for i, ln in enumerate(out) if i > 0]
# generate all variants for voices
variants = ["", "+f1", "+f2", "+f3", "+f4", "+m1", "+m2", "+m3", "+m4", "+m5", "+m6", "+whisper", "+croak"]
voices = itertools.chain(*[[voice + variant for voice in voices] for variant in variants])
cls.INFO = {
"rate": {"minimum": cls.MIN_RATE, "maximum": cls.MAX_RATE, "default": 200},
"pitch": {"minimum": 0.0, "maximum": 1.0, "default": 0.5},
"voices": {"values": list(voices), "default": "default"},
}
return cls.INFO
def __call__(self, *args, **kwargs):
""" Executes command with args, returns data as specified by kwarg['format'] """
if not isinstance(args, list):
args = isinstance(args, basestring) and [args] or isinstance(args, tuple) and list(args)
if getattr(self, 'initial_args', None):
args = self.initial_args + args
self._checks(*args, **kwargs)
# Generate command arg mask from *args with some black pymagic
cmdf = self.cmd+' '+' '.join(['{}' for i in xrange(len(args))])
logging.debug("Command: %s %s %s %s", self, self.cmd, args, kwargs)
#print "Command: %s %s %s %s" % (self, self.cmd, args, kwargs)
ofilter = kwargs.pop('ofilter', getattr(self, 'ofilter', None))
ret_type = kwargs.pop('ret', None)
binary = kwargs.pop('binary', True)
mkcmd = binary and iterpipes.bincmd or iterpipes.linecmd
itercmd = mkcmd(cmdf, *args, **kwargs)
ret = ''
if kwargs.get('error'):
return iterpipes.check_call(iterpipes.bincmd(cmdf, *args, **kwargs))
elif ret_type == bool:
try:
iterpipes.check_call(iterpipes.bincmd(cmdf, *args, **kwargs))
return True
except iterpipes.CalledProcessError:
return False
elif ret_type == int:
return iterpipes.call(iterpipes.bincmd(cmdf, *args, **kwargs))
else:
for buf in iterpipes.run(itercmd):
ret += str(buf)
if ofilter:
ret = ofilter.load(ret)
return ret
def CreatePipFreezeRequest( self ):
"""The property to call the commandline, using an iteration from iterpipes run command.
The rest of overloading definition from PipFreezeDict __setitems__ will by handle by property
GetPipRunCmd, this one simply call the command and put it a queue-list until a iteration
mechanism read from this run statement ."""
self.pip_freeze = run( linecmd( self.PipCommand ) )
