Merging in months of code changes #1
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To do this, run
make QSUBBERLOCAL=--local [TARGETS]
running locally should allow output to go to the screen, which is easier
than looking up the log files, if they even get saved.
Major problem is that this is perturbed by different maternal deposition. So I'm going to start working on HybridUtils to deal with that in a saner way.
More flexible (includes t-tests and a more simplistic cutoff), and automatically treats the different genotypes separately.
This probably should just happen in the script that's dedicated to it, to save time when it's not needed.
Only the best bug fixes.
This way is more consistent, and probably easier to understand what's going on.
Progress bar works by either using the progressbar iterator, or a lambda that returns its input transparently. Try to do the right thing with multiprocessing--generate a pool if needed, but otherwise use single-threading (which is better for tracking errors)
Answer: not really. This is somewhat surprising...
Since I need to know whether something is on X pretty often, this seems worth spinning out.
Some version of ASEr adds a header line with the number of reads. So Ignore that.
It's actually a bit simpler to keep them as strings, and then I can just get a CLU's identity by .split()ing on colons
Notes from the week of 2/09/2018 will be especially helpful here. It seems like taking the autocorrelation at several different strides, then finding where the mean of those is non-zero turns up ~90 exons from ~30 genes with spatial splicing.
Print the stage numbers as well, so I can run multiple times and generate all the files without them clobbering each other
Including finding the correlation with maternal expression, and calculating a p-value for that correlation, since individual cases might be skewed by the spectrum of values.
Maybe I don't want 0 to be 0, but instead the minimum of the figure.
Conflicts: FindAutocorrPSI.py
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Both major (new splicing figure), and minor (smoother running on the cluster)