Improved Python 2.x functionality and added Nesoni

MasterFASTA now differentiates between Python 2.x and 3.x and switches
between raw_input and input respectively for user input commands. A new
command lien argument has been added. It requires pysam and Nesoni to be
installed and takes arguments as follows: -n, --nesoni
folderToStoreResults referenceDirectory fileToAlign.fasta. This function
runs a SHRiMP alignment and then filters, sorts, and indexes the results
as the file newalignments.sorted.bam. Nesoni has a similar command but
personal experience has shown that Nesoni's version of the command is
dysfunctional so MasterFASTA now includes a work around to solve the
problem.