bioperl/bioperl-run — pull request #9 by daisieh (2012-09-07 22:51:07+00:00)
Title: Refactoring code, adding Batchfile.pm

I reorganized the code so that the child modules of Base.pm (FEL.pm, REL.pm, Modeltest.pm, SLAC.pm) did not have to repeat the same code blocks over and over again. The redundancies made it really hard to debug, because although a bug might only be noticed in FEL->run, for example, it actually affects all of the classes because they all repeat the same buggy code.

I also rewrote run for Base.pm to more gracefully deal with errors caused by HYPHY unexpectedly dying (as in the current OSX Lion MP problems). The run output is now stored into a file in the temp directory for easy debugging if you save the tempfiles.

I added proper parsing of output for Modeltest and REL and fixed a bug in Modeltest where it was no longer running properly because HYPHY was expecting the names of output files.

Finally, I added a new child module, BatchFile, that allows you to run any custom batch file you want to specify, not just the four handled by the existing modules.