Pipes and Filters (Shell)
You’re working on a large project trying to predict diversity
hotspots. Another
member of your collaborative team has produced a series of files that
contain lists of areas that resulted from a series of modeling
exercises. Each filename begins with the word area.
Your programmer has whipped up a small python script called
rich_pred.py that takes a single file containing a list of areas,
one per line, and returns the area and the predicted richness based on
the functions and approach given in the Species Area Relationship problem.
Your team is, of
course,
using version control and all of the relevant files are in the
repository. Navigate to the main working directory for your repository
and update it from the command line using svn update. This will place
the necessary files in your main directory. Move the files into the
directory you created for this assignment by either using svn move
filename new_locationor by right clicking on the file in SmartSVN and
selecting Move.
Your job is to take all of these files, run them through the python code
and produce a single list of the areas and associated richness
predictions from all of the sites combined. This list should be sorted
from the smallest area to the largest area, should only include unique
values, and should be stored to a file called
predicted_diversities.txt. You could cut and paste the files
together, run them through the Python code, and then do some post
processing to get the list looking right, but new files are going to be
showing up constantly, and besides, this can be readily accomplished in
one line using the shell. Once you’ve figured out the necessary shell
commands put them in a text file and save it as
predict_richness.sh. Test to make sure everything is working by
running it using the command bash predict_richness.sh. Commit the
new shell program and the resulting data file to the repository.
Email me when you are done with this problem so that I can update your repository for Problem 3.
Optional: Modify your own code from the Species Area Relationship problem.
to create your own version of rich_pred.py instead of using the one
in the repository. One easy way to deal with stdin is to use
fileinput.input(). Move
the equations back into the body of the code so that it’s just a single
self-contained unit. Overwrite the version of rich_pred.py from the
repository and commit the new version.