picrust/picrust — pull request #138 by zaneveld (2013-08-12 21:46:23+00:00)
Title: Addresses Issue #117 Add metagenome confidence intervals

The current implementation incorporates uncertainty due to errors in genome prediction, and uses that uncertainty to generate 95% confidence intervals and variances for the metagenome predictions.

NOTE: due to a mismatch in the current version of the pre-calc'd count table and variance table I could only do testing at the script level and on a small synthetic example. I'm raising an issue for this, but before 1.0 we need to fix the precalc'd files and do a biological test to benchmark speed.

Changes:
-- new variance prediction code
-- new test code
-- abstracted out the script code for file IO so it could be reused for variance input/ouput as well as count tables.
variance tables will use user-input Greengenes version in the same way as count tables, but expect the variance suffix before .biom.
-- Modified the user interface to allow for input of custom variance tables (parallel to how count tables currently work).
-- added example inputs and outputs. I noticed that some old example inputs and outputs were stalling out prior to starting work, but this is already a large PR, so I think we should address this as a separate issue. For now added a custom ids example that runs rapidly.