Sillymap

A silly implementation of a short read mapper for the course DD3436.

Installation

 pip install sillymap

Example

$ sillymap index
This should index your input fasta

$ sillymap map
This should map your sequences against an index

Course goals and content

• Distributed project handling, including using version control system for source code.
  • Git
  • Github
  • Pypi
  • bioconda
• Important libraries in Python.
  • Pandas
  • Biopython
  • scikit-bio
  • Jupyter notebook
  • Matplotlib
• Efficient programming in Python.
  • Numpy
  • Scipy
  • profiling
  • Pypy
• Parallel programming in Python.
  • threads
  • multiprocessing
  • MPI
• Efficient debugging.
  • ipdb

Assignments

Assignment 1: A repository on Github with a Readme, license and setup.py. The program itself only prints a friendly message. Bonus: Travis CI.

Assignment 2: A release on github where the program can map a few exactly matching short reads against a longer sequence, using the burrows wheeler transform and the FM-index (http://alexbowe.com/fm-index/) where rank can be stored as the table Occ in (https://en.wikipedia.org/wiki/FM-index). This assignment should include a test suite.

Assignment 3: Using the test suite for assignment 2, modify the code to make it run faster/more efficiently. Create two versions:

1. Make it run with pypy.
2. Using numpy, scipy or other libraries to speed up the code.

Both scripts should pass integration tests in Travis.

Make a report explaining the optimizations and the improvements.

Assignment 4: Parallelize the code using both:

1. Multiple cores on one computer.
2. Using multiple computers (MPI).

Make a report explaining the optimizations and the improvements.