workingDir=os.getcwd()
chkPointName = None
outFile = file(os.path.join(workingDir,outFastaName),'a')
qsubOptions=''
# complete restart
timer.mark('fastaSplit')
if not RESUME:
startName = originalFasta
inFileName = startName
seqSize = os.stat(originalFasta).st_size
partCt = seqSize/seqSliceSize +1
seqSliceNames = fasta.splitFasta(originalFasta,partCt,tmpDir=workingDir)
tmpf=file(faNameFile,'w')
tmpf.write('\n'.join(seqSliceNames))
tmpf.close()
# reuse split files
if RESUME:
seqSliceNames = []
tmpf = file(faNameFile)
for l in tmpf:
try:
print
seqSliceNames.append(
os.path.join(os.getcwd(),
os.path.split(l.rstrip())[1]))
except:
if argProblem:
print __doc__
return(-1)
if maxRec != None:
fn,=args
recCt=fasta.fastaCount(fn)
count = recCt/maxRec + int(recCt%maxRec!=0)
else:
count,fn= args
count = int(count)
nG = niceName(fn,count)
fasta.splitFasta(fn,splitCt=count,nameGenerator=nG)
return(0) # we did it!
def niceName(rootName,maxN):
n=0
fmt = '_%%0%dd' % int(ceil(log10(maxN)))
base,ext = os.path.splitext(rootName)
while True:
name=base+ fmt% (n) + ext
yield file(name,'w'),name
n+=1
def submitBlast( self, thingToBlast, dbPath, N=12, parameters="-p blastn", formatParameters="-m 8", prefix="GrBl"):
"""Initiates a BLAST job with the given parameters.
thingToBlast can be:
- a path to a FASTA file
- anything or list of things that evaluates to a valid FASTA string(s) when the str() method is applied. (this includes fasta.Record objects)
N is the maximum number of parallel BLASTs to execute.
(the sequences will be split up into at most N files.)
parameters can be either an explicit parameter string to append to the blast call (ie. '-p blastn -b 3')
or a dictionary of { parameter:value } pairs, which will be translated to '-parameter1 value1 -parameter2 value2'
submitBlast returns a list of the names of the threads which are running this Blast.
"""
# Store for database use
self.parameters = parameters
self.dbPath = dbPath
############################
# Build the query
queryPath = None
if isinstance( thingToBlast, str ) and os.path.lexists( thingToBlast ): # path to a FASTA file
queryPath = thingToBlast
self.queryFile = queryPath
elif isinstance( thingToBlast, (tuple, list) ):
( of, queryPath ) = fasta.mystemp( suffix='.fasta', dir=self.tmpDir )
for elt in thingToBlast:
of.write(str(elt) + "\n")
of.close()
self.tempFiles.append( queryPath )
else:
( of, queryPath ) = fasta.mystemp( suffix='.fasta', dir=self.tmpDir )
of.write(str(thingToBlast))
of.close()
self.tempFiles.append( queryPath )
############################
# Split the query
queryFiles = fasta.splitFasta( queryPath, N, tmpDir=self.tmpDir )
self.tempFiles = self.tempFiles + queryFiles
############################
# Build the BLAST line
blastLine = "%s %s -d %s" % ( self.blastPath, formatParameters, dbPath )
if isinstance( parameters, str ):
blastLine = blastLine + " " + parameters
else:
parameterStrings = map( lambda x: "-%s %s" % ( x, parameters[x] ), parameters.keys() )
blastLine = blastLine + " " + " ".join( parameterStrings )
threads = []
for qf in queryFiles:
outfile = qf.replace(".fasta",".br")
self.tempFiles.append( outfile )
command = "%s -i %s -o %s" % ( blastLine, qf, outfile )
thread = self.submitThread( command, qrshArgs="-l arch='fbsd-amd64'", prefix=prefix )
#thread = self.submitThread( command, qrshArgs="-l arch='fbsd-amd64' -l mf=1.0G" )
self.activeQueries.append( ( thread, outfile ) )
threads.append( thread )
return threads