Reproducible Bioinformatics with Python
Author(s): Ken Youens-Clark
Publisher: O'Reilly Media, Inc., Year: 2021
Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and postdoc researchers who've never learned basic programming skills. This practical guide shows how to exploit the best parts of Python for solving problems in biology while also creating documented, tested, reproducible software.
Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates how to write effective Python code and how to use tests to write and refactor scientific programs. You'll learn the latest Python features and tools--such as linters, formatters, type checkers, and tests--to write documented and tested programs.
- Create command-line Python programs that document and validate parameters
- Write tests to verify refactor programs and confirm they're correct
- Address bioinformatics ideas using Python data structures (strings, lists, and sets) and modules such as Biopython
- Create reproducible shortcuts and workflows using makefiles
- Parse essential bioinformatics file formats such as FASTA, FASTQ, and SwissProt
- Find patterns of text using regular expressions
- Use higher-order functions in Python like filter() and map()
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