Make Multigenome now makes genomes for appropriate pairs of genomes

With the new run of data, I think I'll try just mapping to the species that I
know are there.  This should make the downstream stuff even easier/faster.
Hooray!
Explicitly output sample name in AssignRead2
Spin off the read mapping to a separate script

In the big data run, I'm going to want to have a separate configuration
file, as well as not run the cuffdiff until I can assign some sort of
reasonable "replicates", depending on exactly what the hell I mean by
that. So I separate the cuffdiff call until later, and in the mean time,
simplify all the read maping such that it should work sanely.
Merge branch 'Fall2012' of github.com:petercombs/EisenLab-Code into Fall2012
Ignore configuration files
Remove nonfunctional, commented out code
Changes to do_research based on re-divided code
Combine GTF files in MakeMultigenome
Bug fixes based on first dry run
Merge branch 'Fall2012' of github.com:petercombs/EisenLab-Code into Fall2012
Move config variables into a holder object

This is done to inflate my pylint scores.  Otherwise, should have no
effect on the shape of the code.

The one change I've made to the function is to calculate the sequence
directory, then add in the 'R1' or 'R2', to be explicit that both ends
should be in the same directory.
Use Namespaces for internal variables

It turns out that object()s won't let you set their attributes.  At any
rate, the Namespace from argparse seems to have nice string
representations as well.
Only do cufflinks on Base species, and other pylint fixes

Use the base_GTF argument to give the path to the GTF for the base
species only.  I suspect this will speed up the cufflinksing, which
seems to be a moderate bottleneck, at least in the dry-run testing I've
done.

I've also moved more variables into their own Namespaces, creating a
TEMP namespace for names that get reusused willy-nilly.
Remove trailing whitespace
Minor bug fixes

With the Namespaces to write out to a pickle file, I had a bunch of
names for different classes of data, but I failed to be consistent about
where they were coming from.  That's fixed, and it now runs.
Ignore big datafiles and dryrun related stuff
Find readfiles on the fly

Rather than getting all the readfiles in advance, for each sample in the
config file, calculate the read files for that sample at the last
possible moment (i.e. before doing tophat).  This will allow us to start
doing the tophat as the files are being downloaded, which could save a
few hours.
Deal with gzipped files as well

To save space on the HD, have MapReads unzip the files before doing
tophat (if necessary), and then re-zip them when it's done (without
respect to whether they were zipped before hand).
Keep temporary files in tophat runs
AssignReads2 now deals with PE files

I can't guarantee it does it in the sanest, or even correct-est possible
way, but it seems to work for the moment.