Week 2

CMEE coursework for week two: Biological Computing in Python I.

Contents

Lessons

• basic_io.py
  • Basic demonstration of input and output in python.
• basic_csv.py
  • Manipulating csv files using the csv package.
• boilerplate.py
  • Introduction to writing functions.
• using_name.py
  • Clarifying the use of name/main.
• sysargv.py
  • An example of using system arguments.
• scope.py
  • Usage of global and local variables.
• control_flow.py
  • An example in control flows.
• cfexercises1.py
  • Control flow exercise 1.
• loops.py
  • Introduction to loops.
• oaks.py
  • A comparison of loops and list comprehensions.
• debugme.py
  • A script to run using the python debugger.

Practicals

• cfexercises2.py
  • Some functions and modules in python.
• lc1.py
  • An exercise in list comprehensions (part 1).
• lc2.py
  • An exercise in list comprehensions (part 2).
• dictionary.py
  • Populates a dictionary to map oder names to sets of taxa.
• align_seqs.py
  • Aligns DNA sequences using one input txt file.
• align_seqs_fasta.py
  • Aligns DNA sequences using any two input fasta files.
• align_seqs_better.py
  • Aligns DNA sequences and pickles the highest scoring alingnment in addition to equally good scores.
• oaks_debugme.py
  • An exercise in debugging using doctests.

Authors

• Hannah O'Sullivan

License

I don't have one

Acknowledgments

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