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 )