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CODING_GUIDELINES.md

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QUAST Coding Guidelines

Project Structure

Below are the key project directories and their content.

  • root directory (.)

    • main executable files such as quast.py and metaquast.py
    • documentation files such as LICENSE.txt and manual.html
    • installation scripts such as install.sh and setup.py

  • quast_libs - all essential QUAST modules for assembly preprocessing, metrics computation and reporting. The largest modules have their own subdirectories inside, e.g., ca_utils for contig analysis.

    • qconfig.py - storage of all constants, global variables, and option default values. This file also defines QUAST help message
    • qutils.py - common functions used across various modules
    • log.py - logging functions
    • reporting.py - defines the content and order of metrics in all reports (text, PDF and HTML)

  • external_tools - third-party tools used in the QUAST pipeline such as Red (repeat detector), KMC (k-mer counter). Note that the most essential external tools, such as minimap2 (contig aligner) or GeneMark (gene predictor) are stored under quast_libs.

  • test_data - sample test files such as a reference file, assemblies, genes annotation, etc

Coding Style/Conventions

  • The code mainly follows the standard PEP8 Style Guide for Python Code. In particular, this includes using only 4 spaces for indentation, and never tabs.
  • QUAST code is currently compatible with Python 2.5-2.7 and Python 3.5+. The support for Python 2.5-2.6 will be dropped in the next major release. Python 2.7 support will also be deprecated in the near future.

Documentation

  • Please use inline comments to describe non-trivial code. An even better strategy would be designing your code to comment itself.
  • New functionality and quality metrics should be described in the manual.
  • It is also essential to add a brief description of new metrics to the QUAST glossary in quast_libs/html_saver/glossary.json. The glossary content is appended to all HTML reports and is used for tooltips.

Tests and Test Data

  • Key test data is located in test_data and is used with standard QUAST test commands ./quast.py --test, ./metaquast.py --test and more advanced ./quast.py --test-sv, ./metaquast.py --test-no-ref. Please check that your modifications to the code do not break these essential tests.
  • More test data and test scripts are located in tc_tests/data/. To comprehensively test your changes, please run ./tc_tests/test_everything.sh. Ideally, it should be several runs with different Python versions, e.g. ./tc_tests/test_everything.sh python2 and ./tc_tests/test_everything.sh python3 if python2 and python3 are valid Python interpreters in your system. This notice is valid until we completely abandon Python2 support.

Logging

Please avoid using print() for printing messages, warnings and errors. Instead use the QUAST logger like the following.

from quast_libs.log import get_logger

logger = get_logger(qconfig.LOGGER_DEFAULT_NAME)
logger.info('Sample info message')
logger.warning('Sample warning')
logger.error('Non-critical error')
logger.error('Critical error', exit_with_code=1)

Recommendations

  • We recommend using PyCharm for the QUAST development. In particular, this IDE supports code reformating to matching the PEP8 standard and also helps to maintain simultaneous Python2 and Python3 compatibility.

Questions and Suggestions

Please post all your questions regarding these Guidelines and suggestions to its improvement to our public discussion forum. You may also write a private email to [email protected].