Introduction -to- Ecology
A course covering population, community, and ecosystem ecology for undergraduates
We have data on bird communities that we’ve collected that we need to analyze. The data has three columns, a date, a common name, and a count of the number of individuals.
2013-03-22 bluejay 5
2013-03-22 mallard 9
2013-03-21 robin 1
Download the data files using the curl command:
curl -O http://www.programmingforbiologists.org/data/data_drycanyon_2013.txt
curl -O http://www.programmingforbiologists.org/data/data_greencanyon_2013.txt
curl -O http://www.programmingforbiologists.org/data/data_logancanyon_2013.txt
We want to count the total number of individuals of each species that were seen in each data file. We could solve this problem ourselves, but our lab mate has already written some code that does this. Instead of rewriting the code ourselves we can simply add it to a pipeline. Let’s go ahead and download the file:
curl -O http://www.programmingforbiologists.org/code/species_counts.py
To run this code we need to tell the shell to run it using python, which we do by giving it the name of the program that will run it, then the name of our program, and then the input.
python species_counts.py data_greencanyon_2013.txt
This can then be integrated into our pipeline. So if we want to sort based on the total number of individuals:
python species_counts.py data_greencanyon_2013.txt | sort -k 2 -n
This is great for a single datafile with a particular name, but we’ve been
collecting data on birds from a number of different places and we’d like to
conduct all of these analyese simultaneously. Write a simple for loop that loops
over all of the files in the current directory that have the general form of
data_*.txt, prints out the name of the datafile, and then runs
species_counts.py on the datafile. Save this in a text file called all_species_counts.sh.