More bash commands

[mpesesky]

We should carry the option to output bash commands rather than run everything from within the python script through to the analysis, including statistical analysis and data extraction.

[dacb]

The first component of this (outputting scripts for analysis) is in this commit: e391076

We'll have to write the extraction code still, but that might be pure pandas and python if we use tsv/csv or even hdf files vs. a mysql database.