Unicycler tests

This page briefly describes the tests written to check Unicycler. Users of Unicycler are probably uninterested in this stuff, but if you are a Unicycler developer, then read on!

All tests are run from the root Unicycler repository (i.e the directory which contains unicycler-runner.py).

Unit tests

These tests check various functions in Unicycler's code and should complete fairly quickly.

To run unit tests: python3 -m unittest

Random sequence assembly test:

This test:

• generates simple random sequences
• makes fake reads from those sequences
• assembles those reads with Unicycler
• verifies that Unicycler's output looks correct

It runs indefinitely (i.e. will need to be stopped with Ctrl-C).

To run random sequence assembly tests: python3 test/random_sequence_assembly_test.py

Overlap removal test:

This test:

• generates sequences with many repeats
• makes fake reads from those sequences
• assembles those reads with SPAdes
• runs the AssemblyGraph.remove_all_overlaps function on the SPAdes graph

It is designed to test two things:

• whether overlap removal is successful
• overlap removal performance

It runs indefinitely (i.e. will need to be stopped with Ctrl-C).

To run overlap removal tests: python3 test/overlap_removal_test.py

Build test:

This test:

• runs Unicycler's Makefile using a variety of compilers
• runs unicycler_align to make sure it works
• displays the results in a table

Compilers earlier than GCC 4.9.1 and Clang 3.5 are expected to fail, but versions after that should succeed.

To run build tests: python3 test/build_test.py