def filterRedundantMatches( inFile, outFile ):
"""
When a pairwise alignment is launched ~ all-by-all (ie one batch against all chunks),
one filters the redundant matches. For instance we keep 'chunk3-1-100-chunk7-11-110-...'
and we discards 'chunk7-11-110-chunk3-1-100-...'.
Also we keep 'chunk5-1-100-chunk5-11-110-...' and we discards
'chunk5-11-110-chunk5-1-100-...'.
For this of course the results need to be sorted by query, on plus strand,
and in ascending coordinates (always the case with Blaster).
"""
inFileHandler = open( inFile, "r" )
outFileHandler = open( outFile, "w" )
iAlign = Align()
countMatches = 0
tick = 100000
while True:
line = inFileHandler.readline()
if line == "":
break
countMatches += 1
iAlign.setFromString( line )
if "chunk" not in iAlign.range_query.seqname \
or "chunk" not in iAlign.range_subject.seqname:
print "ERROR: 'chunk' not in seqname"
sys.exit(1)
if int(iAlign.range_query.seqname.split("chunk")[1]) < int(iAlign.range_subject.seqname.split("chunk")[1]):
iAlign.write( outFileHandler )
elif int(iAlign.range_query.seqname.split("chunk")[1]) == int(iAlign.range_subject.seqname.split("chunk")[1]):
if iAlign.range_query.getMin() < iAlign.range_subject.getMin():
iAlign.write( outFileHandler )
if countMatches % tick == 0: # need to free buffer frequently as file can be big
outFileHandler.flush()
os.fsync( outFileHandler.fileno() )
inFileHandler.close()
outFileHandler.close()
def updateScoresInFile( inFile, outFile ):
inHandler = open( inFile, "r" )
outHandler = open( outFile, "w" )
iAlign = Align()
while True:
line = inHandler.readline()
if line == "":
break
iAlign.reset()
iAlign.setFromString( line, "\t" )
iAlign.updateScore()
iAlign.write( outHandler )
inHandler.close()
outHandler.close()
def retrieveInitialSequenceHeadersForAlignFile( self, dNew2Init ):
inFileHandler = open( self._inFile, "r" )
outFileHandler = open( self._outFile, "w" )
a = Align()
while True:
line = inFileHandler.readline()
if line == "":
break
a.setFromTuple( line.split("\t") )
nameToBeReplaced = a.range_query.seqname
if dNew2Init.has_key( nameToBeReplaced ):
a.range_query.seqname = dNew2Init[ nameToBeReplaced ]
nameToBeReplaced = a.range_subject.seqname
if dNew2Init.has_key( nameToBeReplaced ):
a.range_subject.seqname = dNew2Init[ nameToBeReplaced ]
a.write( outFileHandler )
inFileHandler.close()
outFileHandler.close()
