wrapped Augustus commands in file test to skip if already done

This is also something that would be better handled by a make file, but I'm somewhat
stuck with this for now, and this is a step that I don't want to rerun unless I have to
as it takes hours
added code to remove gap characters from the sequences
added code to create any missing directories
added script to translate Exonerate results and changed header formatting

I modified the ryo argument to Exonerate to format the header line of the fasta sequences
to be Species_jgi|Copci|gene_family

I also added my script for translating fasta sequences from STDIN and piped the Exonerate output
thru it
modified to add folder name to blast query
added the reference seqs to the prereqs for homolog extraction
modified to loop thru Copci files rather than raw JGI files
added reference genes and raw reads as prereqs for scores file