Changed the format from GenBank to Fasta and corrected the outfile opening so that it works correctly when a filename is specified

Script was written to print to STDIN or to a named file, but the writing to a named file
was not working because I got a message saying "file does not exist"
This is because for SDTIN the open statement does not require the ">" but for a named file it does
The script now checks for this and opens the file appropriately
Corrected problem with smart_consensus where Ns were being added instead of gaps in cases all sequences had Ns at a position

this was caused by situations where some sequences aligned entirely before an alignment
position and all others aligned completely after it.

This caused Ns to be inserted instead of gaps. Since there were non-Ns before and after,
these were not converted to gaps when pad ends was run on the consensus sequence.
I've now fixed this so that gaps are added instead of Ns (so it's no longer necessary to
run pad ends on the consensus sequence). However, this does mean that if there are truly
Ns in all of the sequences at an internal alignment position, that position will be turned
into a gap. This is probably an unlikely situation and wouldn't make all that big a
difference anyway (though it might screw up the coding frame)
Modified to allow start, end and strand to be specified by an optional OrfPredictor outfile

I also removed the code to write an exon feature covering the entire sequence length
because I'm using cufflinks to infer the exon.