blast2graph.py now normalizes each graph 5 different ways (+1 raw graph)

Following renewed debate within our group, I expanded the number of
normalization methods implemented in, and output by, blast2graph.py. Previous
versions produced only two graphs per metric: one untouched, save for removal
of self-hits and restoration of BLAST-rounded E-values, and one normalized by
multiplying each edge by a ratio of the average edge weight across the entire
graph over the average edge weight between the corredponding pair of organisms.

blast2graph.py (which I should probably get around to renaming blast2graphs.py)
now outputs 30 different graphs, corresponding to two different representations
of five different metrics normalized two different ways in addition to the set
of unnormalized graphs. The new representation of each graph is the conversion
of each edge weight into a fraction or multiple of the mean graph edge weight.
This "dimensionless" variant is now produced in addition to the original set,
and facilitates a more direct comparison of edge weights across different
metrics.

The new normalization procedure removes self-hits before calculation of the
graph and inter-organism averages. These graphs are labelled "norm_wo", the
original normalized graphs are labelled "norm_wi", and the unnormalized
(previously "raw") graphs are now labelled "no_norm".

Signed-off-by: trgibbons <ted.codes@gmail.com>
Adding wrapper script for the Expanded CEGMA KOGs analyses

This is a now-heavily modified fork of the original cegma_pipeline.sh script.
This version has been updated to use the most recent version of blast2graph.py.

Signed-off-by: Ted Gibbons <ted.codes@gmail.com>
Updated mcl2rtab.py and ClusteringBarcharts.R to support updated blast2graph.py

The latest version of blast2graph.py introduced new metric names, a new
parameter (the presence or absence of dimensions), and a modified scheme for
naming files. These versions mcl2rtab.py and ClusteringBarcharts.R now support
this updated version of blast2graph.py.

Signed-off-by: Ted Gibbons <ted.codes@gmail.com>