def _para(self, *paraArgs):
"""ssh to the remote machine and run the para command. paraArgs are
passed as arguments to the para command. Returns stdout as a list of
lines, stderr in ProcException if the remote program encouners an
error. There is a possibility for quoting hell here."""
remCmd = "cd " + self.paraDir + "; para " + " ".join(paraArgs)
fileOps.prLine(sys.stderr, "ssh ", self.paraHost, " ", remCmd)
return procOps.callProcLines(
["ssh", "-o", "ClearAllForwardings=yes", self.paraHost, remCmd])
def dump(self, fh, desc=None):
self.__calcParams()
if desc != None:
prLine(fh, desc)
prLine(fh, " data: len: ", len(self.data), " min: ", self.data.min, " max: ", self.data.max)
prLine(fh, " bins: num: ", self.numBins, " size: ", self.binSize, " min: ", self.binMin, " max: ", self.binMax)
prLine(fh, " use: num: ", self.numBinsUse, " size: ", self.binSizeUse, " min: ", self.binMinUse, " max: ", self.binMaxUse,
" floor: ", self.binFloorUse, " ceil: ", self.binCeilUse)
def dump(self, fh, desc=None):
self.__calcParams()
if desc != None:
prLine(fh, desc)
prLine(fh, " data: len: ", len(self.data), " min: ", self.data.min,
" max: ", self.data.max)
prLine(fh, " bins: num: ", self.numBins, " size: ", self.binSize,
" min: ", self.binMin, " max: ", self.binMax)
prLine(fh, " use: num: ", self.numBinsUse, " size: ",
self.binSizeUse, " min: ", self.binMinUse, " max: ",
self.binMaxUse, " floor: ", self.binFloorUse, " ceil: ",
self.binCeilUse)
def prExceptions(er, ex):
"print and exception and any recorded ones"
sys.stdout.flush()
sys.stderr.flush()
fh = sys.stderr
fileOps.prLine(fh, "\n"+strOps.dup(78, '='))
fileOps.prLine(fh, "Unexpected exception:")
fileOps.prLine(fh, ProcException.formatExcept(ex))
for e in er.errors:
fileOps.prLine(fh, strOps.dup(78, '-'))
fileOps.prLine(fh, ProcException.formatExcept(e))
fileOps.prLine(fh, strOps.dup(78, '^'))
sys.stderr.flush()
def dump(self, fh):
"print content to file"
prLine(fh, "query: ", self.qSeq)
prLine(fh, "target: ", self.tSeq)
for blk in self:
blk.dump(fh)
def dump(self, fh):
"print content to file"
prLine(fh, "\t> query: ", self.q)
prLine(fh, "\t target: ", self.t)
def prExceptions(er, ex):
"print and exception and any recorded ones"
sys.stdout.flush()
sys.stderr.flush()
fh = sys.stderr
fileOps.prLine(fh, "\n" + strOps.dup(78, '='))
fileOps.prLine(fh, "Unexpected exception:")
fileOps.prLine(fh, ProcException.formatExcept(ex))
for e in er.errors:
fileOps.prLine(fh, strOps.dup(78, '-'))
fileOps.prLine(fh, ProcException.formatExcept(e))
fileOps.prLine(fh, strOps.dup(78, '^'))
sys.stderr.flush()