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 )
