Pooled species specific changes
Use AssignReads2 in do_tux

Somehow, this used to be in there, but after approximately a183622c,
this got lost in a merge. Now it's back.  So there, fuckers.

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Attempt to assign names more sanely
AssignReads now splits reads into separate files as well

Uses a defaultdict to read off the species, and make a separate bam-file for
4 each species in the data.  At some point, I should spin off this defaultdict
(a subclass of the Collections version) into a Utilities module, but not
today.
Hunt Dark Matter now incorporates gene expression levels

Previously, the null model was that all the slices would be equal, which
is stupid.  Now, we're assuming that all the slices use each enhancer in
proportion to the total expression, which is clearly wrong, but not a
stupid null model.

Also add in BigWig handling (should work interchangeably with .bam
files, but has never been tested), and an ability to use SIGTERM to skip
the current gene (but not kill the whole program).  SIGKILL still brings
us to a grinding halt.

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#	PlotSigDarkmatter.py
added PlotSigDarkmatter

Reads off the significant/non-significant calls in the HuntDarkmatter
log file, and plots a bar chart (Is this the best idea?) of the
significant genes.

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Merge in changes
Create MakeMultigenome

A program for combining the Flybase genomes into a single multifasta file that
contains all, with species identifiers in front of everything.  Runs without
crashing, but output not yet verified.
Create do_research

This is a master script that should tie everything together.  Ideally,
it will start with the FlyBase reference files, and (some hours or days
later) output all the figures, tables, and other numbers necessary for a
publication.  Also has the option to skip sections during testing.
do_tux now based on multi-genome file
Add in the call to assign multireads
Merge branch 'PAC45' of github.com:petercombs/EisenLab-Code into PAC45
Keep track of ambiguous species

For my purposes, there's not a problem if the ambiguous-ness is between, say,
virilis and persimilis, since I only care about the melanogaster reads.
Similarly, I suspect for Susan's data, she only cares that the read doesn't
come from melanogaster, so having a sense of where these problems lie would be
useful.
Remove the plotting from do_tux

For one thing, it doesn't work on deme, for another, I don't actually care
about it any more, and for a third, it no longer (if ever) really logically fit
in with the tuxedo suite, but instead is its own idea.  Will eventually make a
separate script that makes some/all of the figures.
Sort mel output from AssignReads
Minor readability tweaks
Create do_tux_plotting

This is the plotting section from do_tux.py that got removed a few commits ago,
spun off to its own file.
Merge branch 'PAC45'

Conflicts:
	do_tux.py