Updates to extract_shared_or_unique_otuids.py and filter_biom.py and test scripts.

[akshayparopkari]

Improved functionality to align closely with PhyloToAST modules. Also, updated syntax for Python 2 and 3 compatibility. No documentation updates needed for these change.

Description

• Updated extract_shared_or_unique_otuids.py:
  • Moved assign_otu_membership function to otu_calc module and is now called via otu_calc import.
  • Output parameter --output_dir is changed to positional type from optional.
  • Syntax is Python 2 and 3 compatible.
• Updated filter_biom.py:
  • Switched to using PhyloToAST mapping file reading function from util module.
  • Updated syntax for biom.filter function.
  • Removed unused pandas import.
  • Syntax is Python 2 and 3 compatible.
• Updated API and its test script
  • Updated biom_calc to be compatible with Python 2 and 3.
  • Similar changes for test_biom_calc script.
  • Added missed test.
  • Other minor updates.
• Updated .gitignore:
  • Ignore coverage and other unit testing dot files.

Motivation and Context

#50

How Has This Been Tested?

Local flake8 on Py2 and Py3 env for syntax and unit testing modules on Py2 env.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.