This lesson assumes you have a working knowledge of Python and some previous exposure to the Bash shell.
These requirements can be fulfilled by:
- completing a Software Carpentry Python workshop or
- completing a Data Carpentry Ecology workshop (with Python) and a Data Carpentry Genomics workshop or
- coursework in or independent learning of both Python and the Bash shell.
Bash shell skills
The skill set listed below is covered in any Software Carpentry workshop, as well as in Data Carpentry’s Genomics workshop. These skills can also be learned through coursework or independent learning.
Be able to:
- Identify and navigate to your home directory.
- Identify your current working directory.
- Navigating directories using
cd <subdirectory>, and
This skill set listed below is covered in both Software Carpentry’s Python workshop and in Data Carpentry’s Ecology workshop with Python. These skills can also be learned through coursework or independent learning.
Be able to:
- Perform basic arithmetic operations (e.g. addition, subtraction) on variables.
- Convert strings to ints or floats where appropriate.
- Create a
listand alter lists by appending, inserting, or removing values.
- Use indexing and slicing to access elements of strings, lists, and Numpy arrays.
- Use good coding practices to comment your code and choose appropriate variable names.
- Write a
forloop that increments a variable.
- Write conditional statements using
- Use comparison operators (
>=) in conditional statements.
- Open, read from, write to, and close input and output files.
len()to inspect variables.
The following skills are useful, but not required:
- Apply a function to an entire Numpy array or to a single array axis.
- Write a user-defined function.
If you are signed up, or considering signing up for a workshop, and aren’t sure whether you meet these reqirements, please get in touch with the workshop instructors or host.