Data Science in Omics Introduction
An OMICS Course Part 1: Shell, Organizing and Genomics
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 one of these files using the curl command:
curl -O https://github.com/hoytpr/bioinformatics-semester/data/data-drycanyon-2013.txt
If we wanted to find the least common species in the data file and store that information we could do something like:
sort data-drycanyon-2013.txt -k 3 -n > sorted-counts.txt
head -1 sorted-counts.txt > least-common-species.txt
Now we want to get the most common species at the site. You can do this using
the tail command. Since we don’t need the intermediate sorted_counts.txt
file, use a pipe instead of creating the intermediate file.
Save both the curl command and the one line command for storing the least common
species in a text file called get-most-common-species.sh.