Architecture Overview

Project files and directories


The integron_finder licensing.
The integron finder copy rights holders.
What must be or should not included in the distribution.
The file to red in first.
The requirements need to use integron_finder.
The extra requirements to develop on integron_finder.
The configuration file.
The file to define how to build/install/release/test/… integron finder.


The core of the projects contains integron_finder library The scripts/finder contain the main entry point.
Contains all needed for tests, the tests themselves, are a the top level and the name must start by test_. The data directory contains all data needed to perform the tests. (see Tests for further details)
Contains the documentation write in sphinx. The source directory contains the .rst files, whereas the build directory contains the generated documentation. To know how to contribute or generate documentation see Documentation
Contains the definition file for singularity container.
This directory is generated when a distribution is created (python sdist).

Technical overview

The main entry point is in integron_finder/scripts/ there are 3 functions

intgeron_finder.scripts.main() which is the real main entry point

main call scripts/finder.parse_args() which parse the commandline and generate a config.Config object. and do a loop over replicon and run intgeron_finder.scripts/find_integron_in_one_replicon()

all results are store in a directory named Results_Integron_Finder_<replicon_file_name> this directory is created by intgeron_finder.scripts/find_integron_in_one_replicon() store results in this directory or in a subdirectory call tmp_<replicon_id> these subdirectories will be keep only if --keep-tmp option is set, otherwise they are removed at the end of the intgeron_finder.scripts/find_integron_in_one_replicon()

when all replicons are computed the main function call integron_finder.utils.merge_results() to gather all results files <replicons_id>.integtrons and generate a unique file with these information.

to have details on find_integron_in_one_replicon works see Introduction