def merge(self):
"""merge runs from parallel computations.
returns true if merging was succecss.
"""
if self.isComplete(): return
infiles = glob.glob("%s*" % self.mFilenameProfile)
# remove suffixes
infiles = list(
set([x[:-4] for x in infiles if x != self.mFilenameProfile]))
infiles.sort()
last_nid = None
found = set()
ninput, noutput, nfound, nunknown, nduplicate = 0, 0, 0, 0, 0
tokens = set(self.mFasta.keys())
self.mProfileLibrary = ProfileLibrary.ProfileLibrary(
self.mFilenameProfile, "w")
for filename in infiles:
infile = ProfileLibrary.ProfileLibrary(filename, "r")
for nid, profile in infile.iteritems_sorted():
ninput += 1
if nid in found:
nduplicates += 1
self.warn("duplicate nid: %i in file %s" % (nid, filename))
if nid not in tokens:
nunknown += 1
self.warn("unknown nid: %i in file %s" % (nid, filename))
found.add(nid)
nfound += 1
self.mProfileLibrary.add(nid, profile)
noutput += 1
missing = tokens.difference(found)
if len(missing) > 0:
self.warn("the following nids were missing: %s" % str(missing))
self.info("adding %i missing nids" % len(missing))
for nid in missing:
self.applyMethod(AddaIO.NeighboursRecord(nid, []))
self.info( "merging: parts=%i, ninput=%i, noutput=%i, nfound=%i, nmissing=%i, nduplicate=%i, nunknown=%i" %\
(len(infiles), ninput, noutput, nfound, len(missing), nduplicate, nunknown ) )
self.info("deleting %i parts" % len(infiles))
for infile in infiles:
fn, fi = ProfileLibrary.getFileNames(infile)
os.remove(fn)
os.remove(fi)
return len(missing) == 0 and nduplicate == 0 and nunknown == 0
def merge(self):
"""merge runs from parallel computations.
returns true if merging was succecss.
"""
if self.isComplete(): return
infiles = glob.glob( "%s*" % self.mFilenameProfile )
# remove suffixes
infiles = list(set([ x[:-4] for x in infiles if x != self.mFilenameProfile ]))
infiles.sort()
last_nid = None
found = set()
ninput, noutput, nfound, nunknown, nduplicate = 0, 0, 0, 0, 0
tokens = set(self.mFasta.keys())
self.mProfileLibrary = ProfileLibrary.ProfileLibrary( self.mFilenameProfile,
"w" )
for filename in infiles:
infile = ProfileLibrary.ProfileLibrary( filename, "r" )
for nid, profile in infile.iteritems_sorted():
ninput += 1
if nid in found:
nduplicates += 1
self.warn("duplicate nid: %i in file %s" % (nid, filename))
if nid not in tokens:
nunknown += 1
self.warn("unknown nid: %i in file %s" % (nid, filename))
found.add(nid)
nfound += 1
self.mProfileLibrary.add( nid, profile )
noutput += 1
missing = tokens.difference( found )
if len(missing) > 0:
self.warn( "the following nids were missing: %s" % str(missing) )
self.info( "adding %i missing nids" % len(missing))
for nid in missing:
self.applyMethod( AddaIO.NeighboursRecord( nid, [] ) )
self.info( "merging: parts=%i, ninput=%i, noutput=%i, nfound=%i, nmissing=%i, nduplicate=%i, nunknown=%i" %\
(len(infiles), ninput, noutput, nfound, len(missing), nduplicate, nunknown ) )
self.info( "deleting %i parts" % len(infiles) )
for infile in infiles:
fn, fi = ProfileLibrary.getFileNames( infile )
os.remove( fn )
os.remove( fi )
return len(missing) == 0 and nduplicate == 0 and nunknown == 0
def startUp(self):
if self.isComplete(): return
if self.mAppend:
self.mProfileLibrary = ProfileLibrary.ProfileLibrary(
self.mFilenameProfile + self.getSlice(), "a")
self.mContinueAt = self.mProfileLibrary.getLastInsertedKey()
self.info("processing will continue after %s" %
(str(self.mContinueAt)))
else:
self.mProfileLibrary = ProfileLibrary.ProfileLibrary(
self.mFilenameProfile + self.getSlice(),
"w",
force=self.mForce)
# set default values
self.mProfileLibrary.setLogOddor(
alignlib.makeLogOddorDirichlet(self.mScaleFactor))
self.mProfileLibrary.setRegularizor(
alignlib.makeRegularizorDirichletPrecomputed())
self.mProfileLibrary.setWeightor(alignlib.makeWeightor())
alignlib.setDefaultEncoder(alignlib.getEncoder(alignlib.Protein20))
def outputSummaryProfiles(self):
"""analyse the alignments."""
if not os.path.exists(self.mFilenameProfiles):
return {'nids': 0}
self.mProfileLibrary = ProfileLibrary.ProfileLibrary(
self.mFilenameProfiles, "r")
nids = self.mProfileLibrary.keys()
self.mOutfile.write(">%s\n" % self.mFilenameProfiles)
self.mOutfile.write("nnids\t%i\t%5.2f\n" %
(len(nids), 100.0 * len(nids) / self.mNNids))
return {'nids': len(nids)}
def startUp( self ):
if self.isComplete(): return
###############################################
# create objects for algorithm
alignlib.getDefaultToolkit().setEncoder( alignlib.getEncoder( alignlib.Protein20 ) )
self.mLogOddor = alignlib.makeLogOddorDirichlet( self.mScaleFactor )
self.mRegularizor = alignlib.makeRegularizorDirichletPrecomputed()
self.mWeightor = alignlib.makeWeightor()
alignlib.getDefaultToolkit().setRegularizor( self.mRegularizor )
alignlib.getDefaultToolkit().setLogOddor( self.mLogOddor )
alignlib.getDefaultToolkit().setWeightor( self.mWeightor )
if self.mUsePrebuiltProfiles:
self.mProfileLibrary = ProfileLibrary.ProfileLibrary( self.mFilenameProfiles, "r" )
self.mProfileLibrary.setWeightor( self.mWeightor )
self.mProfileLibrary.setLogOddor( self.mLogOddor )
self.mProfileLibrary.setRegularizor( self.mRegularizor )
else:
self.mProfileLibrary = None
self.mIndexedNeighbours = cadda.IndexedNeighbours( self.mFilenameGraph, self.mFilenameIndex )
self.mChecker = self.checkLinkZScore
self.mHeader = ("qdomain",
"sdomain",
"weight",
"passed",
"qstart",
"qend",
"qali",
"sstart",
"send",
"sali",
"score",
"naligned",
"ngaps",
"zscore" )
self.mAlignator = alignlib.makeAlignatorDPFull( alignlib.ALIGNMENT_LOCAL,
self.mGop,
self.mGep )
# the cache to store alignandum objects
self.mCache = {}
alignlib.setDefaultEncoder( alignlib.getEncoder( alignlib.Protein20 ) )
## initialize counters
self.mNPassed, self.mNFailed, self.mNNotFound = 0, 0, 0
self.mOutfile = self.openOutputStream( self.mFilenameAlignments )
if self.mContinueAt == None:
self.mOutfile.write( "\t".join( self.mHeader ) + "\n" )
self.mOutfile.flush()
self.mStartTime = time.time()
def isComplete(self):
fn, fi = ProfileLibrary.getFileNames(self.mFilenameProfile +
self.getSlice())
return SegmentedFile.isComplete(fi)
def isComplete( self ):
fn, fi = ProfileLibrary.getFileNames( self.mFilenameProfile + self.getSlice() )
return SegmentedFile.isComplete( fi )
