def __init__( self, name="" ):
BioseqDB.__init__( self, name )
seqLength = self.getLength()
if self.getSize() > 1:
for bs in self.db[1:]:
if bs.getLength() != seqLength:
print "ERROR: aligned sequences have different length"
def getClusteringResultsInFasta( self, inFile ):
"""
Write a fasta file whose sequence headers contain the clustering IDs.
"""
dClusterId2SeqHeaders = self.getClustersFromTxtFile()
if self._filterUnclusteredSeq:
dClusterId2SeqHeaders = self.filterUnclusteredSequences( dClusterId2SeqHeaders )
inDB = BioseqDB( inFile )
outFileName = "%s_blastclust.fa" % ( inFile )
outF = open( outFileName, "w" )
for clusterId in dClusterId2SeqHeaders.keys():
memberId = 1
for seqHeader in dClusterId2SeqHeaders[ clusterId ]:
bs = inDB.fetch( seqHeader )
bs.header = "BlastclustCluster%iMb%i_%s" % ( clusterId, memberId, seqHeader )
bs.write( outF )
memberId += 1
outF.close()
def orientInputSequences( self, lSequenceHeadersToReverse, tmpFileName="" ):
"""
Save input sequences while re-orienting those needing it.
@param lSequenceHeadersToReverse: list of headers corresponding to sequences than need to be re-oriented
@type lSequenceHeadersToReverse: list of strings
@param tmpFileName: name of a fasta file (inFileName by default)
@type tmpFileName: string
"""
if self._verbose > 0:
print "saving oriented sequences..."
sys.stdout.flush()
if tmpFileName == "":
tmpFileName = self._inFileName
inDB = BioseqDB( tmpFileName )
outDB = BioseqDB()
for bs in inDB.db:
if bs.header in lSequenceHeadersToReverse:
bs.reverseComplement()
bs.header += " re-oriented"
outDB.add( bs )
outDB.save( self._outFileName )
def dbLongestSequences( num, inFileName, outFileName="", verbose=0, minThresh=0 ):
bsDB = BioseqDB( inFileName )
if verbose > 0:
print "nb of input sequences: %i" % ( bsDB.getSize() )
if outFileName == "":
outFileName = inFileName + ".best" + str(num)
outFile = open( outFileName, "w" )
if bsDB.getSize()==0:
return 0
num = int(num)
if verbose > 0:
print "keep the %i longest sequences" % ( num )
if minThresh > 0:
print "with length > %i bp" % ( minThresh )
sys.stdout.flush()
# retrieve the length of each input sequence
tmpLSeqLgth = []
seqNum = 0
for bs in bsDB.db:
seqNum += 1
tmpLSeqLgth.append( bs.getLength() )
if verbose > 1:
print "%d seq %s : %d bp" % ( seqNum, bs.header[0:40], bs.getLength() )
sys.stdout.flush()
# sort the lengths
tmpLSeqLgth.sort()
tmpLSeqLgth.reverse()
# select the longest
lSeqLgth = []
for i in xrange( 0, min(num,len(tmpLSeqLgth)) ):
if tmpLSeqLgth[i] >= minThresh:
lSeqLgth.append( tmpLSeqLgth[i] )
if verbose > 0:
print "selected max length: %i" % ( max(lSeqLgth) )
print "selected min length: %i" % ( min(lSeqLgth) )
sys.stdout.flush()
# save the longest
inFile = open( inFileName )
seqNum = 0
nbSave = 0
for bs in bsDB.db:
seqNum += 1
if bs.getLength() >= min(lSeqLgth) and bs.getLength() >= minThresh:
bs.write( outFile )
if verbose > 1:
print "%d seq %s : saved !" % ( seqNum, bs.header[0:40] )
sys.stdout.flush()
nbSave += 1
if nbSave == num:
break
inFile.close()
outFile.close()
if verbose > 0:
print nbSave, "saved sequences in ", outFileName
sys.stdout.flush()
return 0
