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F7ABBSJ - Scripting Languages

Code Completion Credits Range Language
F7ABBSJ KZ 2 2C English
Course guarantor:
Radim Krupička
Lecturer:
Tutor:
Tomáš Krajča
Supervisor:
Department of Biomedical Informatics
Synopsis:

The aim of the course is to understand the topic of scripting languages and their applications, to understand their advantages and disadvantages and their complementarity with system languages. Students will become familiar with regular expressions and tools for word processing. The course focuses on the scripting languages within the Unix operating system and the scripting languages Python.

Requirements:

The student's knowledge is tested by continuous assessment through two tests after each block. Each test is graded with 50 points and it is necessary to obtain at least 50% in total, i.e. 50 points/2 tests. The final grade is determined by the number of points obtained and the ECTS scale. The course allows for a maximum of 2 excused absences.

Syllabus of lectures:

Course has no lectures.

Syllabus of tutorials:

1. Scripting languages, advantages and disadvantages, overview of languages, Git

2. Unix shell - scripting, editors, variables, conditions

3. Unix shell - basic programs, task and process management, loops

4. Unix shell - functions, parameter processing

5. Unix shell - Argument parsing, arrays, functions

6. Unix shell - text operations, file handling. Test preparation.

7. Credit test 1

8. Python - introduction, conventions, data types, data structures

9. Python - conditions, functions, variables, loops

10. Python - file handling

11. Python - Pandas, Numpy data processing library

12. Public holiday - Python Scipy library

13. Python matplotlib library, graphical output. Scipy

14. Test preparation. Snakemake and pipelines.

14. Credit test 2

Study Objective:
Study materials:

Mandatory references:

[1] NEWHAM, Cameron a Bill ROSENBLATT. Learning the bash Shell: UNIX Shell Programming. 3rd ed. Beijing: O'Reilly, 2005. ISBN 978-0-596-00965-6.

[2] LUTZ, Mark. Learning Python. Fifth edition. Beijing: O'Reilly, 2013. ISBN 978-1-449-35573-9.

Recommended references:

[1] LANGTANGEN, Hans Petter. Python scripting for computational science. 3rd ed. Berlin: Springer, c2008. ISBN 978-3-540-73915-9.

[2] BURTCH, Ken O. Linux shell scripting with bash. Indianapolis: Developer's Library, c2004. ISBN 0-672-32642-6.

[3] CRAWLEY, Michael J. Statistics: an introduction using R. Second edition. Chichester, West Sussex, UK: John Wiley & Sons, 2014. ISBN 9781118941119.

Note:
The course is a part of the following study plans:
Downloads: