Added Ability to use amino acid sequences as reference file.
Modified run_BLAST to use biopython tBLASTn & BLASTn wrappers
Added parameter to overrider autodetection of fasta file type.
Added helper method to automatically detect Fasta file type. prot/nucl

	modified:   SeqFindR.py
2013-07-16 Nabil-Fareed Alikhan <n.alikhan@uq.edu.au>
 * Added Ability to use amino acid sequences as Virluence factors
 * Added helper method to automatically detect type of sequence file (nucl or pro)
 * Added commandline override option for above auto-detection ( -R )
 * Replaced a number of system calls and pathnames with cross  platform  friendly alternatives
 * Added support for fasta file extensions .fna, .fas, .fa; rather than just
   .fas (For query sequences)$
	modified:   SeqFindR.py
Merge branch 'master' of https://github.com/mscook/SeqFindR

Adding my stuff:
Merged changes
Fixed whitespace
changed name
Added tblastx funcationality (use -X flag)
Merge pull request #5 from happykhan/master

Merged with latest seqfindr - no checking...