Life scientists today urgently need training in bioinformatics skills.
Too many bioinformatics programs are poorly written and barely
maintained, usually by students and researchers who've never learned
basic programming skills. This practical guide shows postdoc
bioinformatics professionals and students how to exploit the best parts
of Python to solve problems in biology while creating documented,
tested, reproducible software.
Ken Youens-Clark, author of Tiny Python Projects (Manning),
demonstrates not only how to write effective Python code but also how to
use tests to write and refactor scientific programs. You'll learn the
latest Python features and tools including linters, formatters, type
checkers, and tests to create documented and tested programs. You'll
also tackle 14 challenges in Rosalind, a problem-solving platform for
learning bioinformatics and programming.
- Create command-line Python programs to document and validate
parameters
- Write tests to verify refactor programs and confirm they're correct
- Address bioinformatics ideas using Python data structures and modules
such as Biopython
- Create reproducible shortcuts and workflows using makefiles
- Parse essential bioinformatics file formats such as FASTA and FASTQ
- Find patterns of text using regular expressions
- Use higher-order functions in Python like filter(), map(), and
reduce()