Reproduciable Science
Lecture notes¶
Exercise¶
Please work in groups of two. During the exercise fill your comments directly in the GoogleDoc file using the link here.
1. Markdown¶
Open Haroopad/MacDown. Explore the markdown editor by yourself. Try to generate titles of different sizes, add plain text and code and save the markdown files as pdf. Use either the features in the insert menu or the cheat sheet.
2. RegEx¶
Download the table from the course website here and open it with the Atom editor. Go to the find and replace section and activate the regex mode.
Remove the ending (_L*) from each fasta header. The cheat sheet might be helpful.
Solution
>([A-Z,0-9]+)_L[0-9]+ >$1
3. Data manipulation¶
Download the table from the course website here. It is a subset of the sex of life database. For each plant species the sexual system is provided.
The goal is to reformat the table from the version you have into the format below.
| Genus | Species | Sexual_system |
|---|---|---|
| Silene | acutifolia | hermaphrodite |
| Silene | adenocalyx | hermaphrodite |
| Silene | aegaea | hermaphrodite |
| Silene | aegyptiaca | hermaphrodite |
| Silene | aellenii | hermaphrodite |
| Silene | almolae | hermaphrodite |
| Silene | alpestris | hermaphrodite |
| Silene | ammophila | NA |
| Silene | amoena | NA |
| Silene | acaulis | non_hermaphrodite |
| Silene | dioica | non_hermaphrodite |
| Silene | latifolia | non_hermaphrodite |
| Silene | vulgaris | non_hermaphrodite |
(1) Write a short log file to describe what you did using your favorite editor or excel.
In the next exercise we going to use R to do the manipulation.