faircloth-lab/phyluce — pull request #1 by jonchang (2012-04-24 19:00:10+00:00)
Title: update process_reads.py

These changes make ```argparse``` properly mark which command line options are required, and adds an option for "initial setup" (which causes the ```make_dirs_and_rename_files``` function to be called). It also makes the ```make_dirs_and_rename_files``` function emit more helpful error messages when they occur.