def CheckLink(self, query_nid, query_from, query_to, sbjct_nid, sbjct_from,
sbjct_to):
"""check, whether link is faithfull.
"""
query_profile = self.GetProfile(query_nid)
query_profile.useSegment(query_from, query_to)
sbjct_profile = self.GetProfile(sbjct_nid)
sbjct_profile.useSegment(sbjct_from, sbjct_to)
alignator = alignlib.makeFullDP(self.mGop, self.mGep)
result = alignlib.makeAlignataVector()
alignator.Align(query_profile, sbjct_profile, result)
if result.getLength() == 0:
query_profile.useFullLength()
sbjct_profile.useFullLength()
return 0, result
if self.mLogLevel >= 3:
print "# --> %i vs %i: score=%5.2f, length=%i, numgaps=%i, row_from=%i, row_to=%i, col_from=%i, col_to=%i" %\
(query_nid, sbjct_nid,
result.getScore(),
result.getLength(),
result.getNumGaps(),
result.getRowFrom(), result.getRowTo(),
result.getColFrom(), result.getColTo())
sys.stdout.flush()
if result.getScore() < self.mMinAlignmentScore:
query_profile.useFullLength()
sbjct_profile.useFullLength()
return 0, result
if result.getScore() > self.mSafetyThreshold * self.mMinAlignmentScore:
query_profile.useFullLength()
sbjct_profile.useFullLength()
return 1, result
z_params = alignlib.makeNormalDistributionParameters()
alignlib.calculateZScoreParameters(z_params, query_profile,
sbjct_profile, alignator,
self.mNumIterationsZScore)
mean = z_params.getMean()
stddev = z_params.getStandardDeviation()
if stddev == 0: stddev = 1
zscore = (result.getScore() - mean) / stddev
if self.mLogLevel >= 3:
print "# --> mean=%f, stdev=%f, zscore=%f" % (mean, stddev, zscore)
sys.stdout.flush()
query_profile.useFullLength()
sbjct_profile.useFullLength()
if zscore > self.mMinZScore:
return 1, result
else:
return 0, result
def checkLinkZScore( self,
query_nid, query_from, query_to,
sbjct_nid, sbjct_from, sbjct_to):
"""check, whether two domains are homologous.
The check is done using a zscore calculation.
"""
result = alignlib.makeAlignmentVector()
query_profile = self.getAlignandum( query_nid )
sbjct_profile = self.getAlignandum( sbjct_nid )
if not query_profile or not sbjct_profile:
self.warn( "could not compute link %s_%i_%i - %s_%i_%i\n" % \
(query_nid, query_from, query_to,
sbjct_nid, sbjct_from, sbjct_to) )
self.mNNotFound += 1
return False, result, ("na",)
query_profile.useSegment( query_from, query_to )
sbjct_profile.useSegment( sbjct_from, sbjct_to )
self.mAlignator.align( result, query_profile, sbjct_profile )
self.debug( "# --> %s vs %s: score=%5.2f, length=%i, numgaps=%i, row_from=%i, row_to=%i, col_from=%i, col_to=%i" %\
(query_nid, sbjct_nid,
result.getScore(),
result.getLength(),
result.getNumGaps(),
result.getRowFrom(), result.getRowTo(),
result.getColFrom(), result.getColTo()))
if result.getLength() == 0:
query_profile.useSegment()
sbjct_profile.useSegment()
return False, result, ("na",)
elif result.getScore() < self.mMinAlignmentScore:
query_profile.useSegment()
sbjct_profile.useSegment()
return False, result, ("na",)
elif result.getScore() > self.mSafetyThreshold * self.mMinAlignmentScore:
query_profile.useSegment()
sbjct_profile.useSegment()
return True,result, ("na",)
z_params = alignlib.makeNormalDistributionParameters()
alignlib.calculateZScoreParameters( z_params,
query_profile,
sbjct_profile,
self.mAlignator,
self.mNumIterationsZScore)
mean = z_params.getMean()
stddev = z_params.getStandardDeviation()
if stddev == 0: stddev = 1
zscore = (result.getScore() - mean) / stddev
self.debug( "--> mean=%f, stdev=%f, zscore=%f" % (mean, stddev, zscore) )
query_profile.useSegment()
sbjct_profile.useSegment()
if zscore > self.mMinZScore:
return True, result, ( "%5.2f" % zscore,)
else:
return False, result, ( "%5.2f" % zscore,)
def CheckLink( self,
query_nid, query_from, query_to,
sbjct_nid, sbjct_from, sbjct_to):
"""check, whether link is faithfull.
"""
query_profile = self.GetProfile( query_nid )
query_profile.useSegment( query_from, query_to)
sbjct_profile = self.GetProfile( sbjct_nid )
sbjct_profile.useSegment( sbjct_from, sbjct_to)
alignator = alignlib.makeFullDP( self.mGop, self.mGep )
result = alignlib.makeAlignataVector()
alignator.Align( query_profile, sbjct_profile, result)
if result.getLength() == 0:
query_profile.useFullLength()
sbjct_profile.useFullLength()
return 0, result
if self.mLogLevel >= 3:
print "# --> %i vs %i: score=%5.2f, length=%i, numgaps=%i, row_from=%i, row_to=%i, col_from=%i, col_to=%i" %\
(query_nid, sbjct_nid,
result.getScore(),
result.getLength(),
result.getNumGaps(),
result.getRowFrom(), result.getRowTo(),
result.getColFrom(), result.getColTo())
sys.stdout.flush()
if result.getScore() < self.mMinAlignmentScore:
query_profile.useFullLength()
sbjct_profile.useFullLength()
return 0, result
if result.getScore() > self.mSafetyThreshold * self.mMinAlignmentScore:
query_profile.useFullLength()
sbjct_profile.useFullLength()
return 1,result
z_params = alignlib.makeNormalDistributionParameters()
alignlib.calculateZScoreParameters( z_params,
query_profile,
sbjct_profile,
alignator,
self.mNumIterationsZScore)
mean = z_params.getMean()
stddev = z_params.getStandardDeviation()
if stddev == 0: stddev = 1
zscore = (result.getScore() - mean) / stddev
if self.mLogLevel >= 3:
print "# --> mean=%f, stdev=%f, zscore=%f" % (mean, stddev, zscore)
sys.stdout.flush()
query_profile.useFullLength()
sbjct_profile.useFullLength()
if zscore > self.mMinZScore:
return 1,result
else:
return 0,result