added code to determine rep. seqs for each corset cluster and write them to orthoMCL directory

AddData.py will determine the member of each corset group with the longest blast hit.
GetData.py will take these sequences and print them out.
I've modified the pipeline to format AA seqs from Transdecoder and write them to AA_Seqs,
then write the output of GetData.py to the compliantFasta folder in orthoMCL with
necessary formatting
minor bug fixes

-have to pass the species name to perl rather than expanding the shell variable within the
perl code

-fixed the base directory

-added code to deal with the name change for KRAUS when preparing files for orthoMCL
modified the code to copy reference AA seqs so that they comply with orthoMCL
modified the code to copy BLUELEAF AA seqs so that they comply with orthoMCL
Added code to filter out blast hits where the query or subject is a redundant seq
added error checking for sequences that are missing from the DB
added scripts for doing read mapping
added code to initialise orthMCL database
added comment about how to speed up script
fixed code to run orthoMCL
first commit
added code to plot histograms of lengths of coding portions of non-redundant sequences

The plots aren't perfect at this point. I would like to figure out how to write the
contig number for each one on the plots, as well as writing the species names inside the
plot with the same colour coding as the plots. Ideally, I would also plot the histogram
for the reference strain behind, but that may be more trouble than it's worth
added code to plot histograms of lengths of coding portions of non-redundant sequences
added code to make venn diagram of overlap of oortholog sets