Add of exchangeable forbidden genes. Now they are a field in SystemOccurence, and that is fed with fill_with_hits and fill_with_cluster functions.
Add info on gene features in print function of genes.
In search_systems.Cluster.save.try_system function, now forbidden genes of a system are considered as part of it for assignment of putative_systems, and can thus be present in 'clear' case of clusters.
Rationalization of system creation during parsing. Now genes of systems_to_parse are also fully filled, which allows to have full 'foreign' genes in other systems, without redefining all their features and asking for the detection of the system to be able to use its full genes.
Remove of a print.
Update of disambiguate_cluster function. The function now works even when forbidden genes are taken into account for the computation of compatible_systems in Cluster.save. The Counter of components'occurrences by compatible system is scanned appropriately, without searching in it for compatible systems that are not considered in disambiguation.
Bug fix in system_parser.system_to_parse and system_parser.parse. Now that all systems to parse are filled, there is now a recursive scan of system_ref to parse in order to have system consistency.
Cleaning in system_parser.system_to_parse and parse. Removal of the old system_to_parse function, and of prints.
Update of gene.__str__.
Update of unit test test_Gene.test_str. Now it corresponds to the new version of Gene.__str__.
Update of unit tests in test_SystemParser: calls to the newly modified function system_parser.system_to_parse, and update of definitions of fake systems for congruence with new parser scheme.
Update of unit tests. Update of definitions of bad_min_genes_required system for congruence with new parser scheme.
Update of unit tests. Update of definitions of fail_invalid_presence system for congruence with new parser scheme (appropriate system_ref).
Update of unit tests. Update of definitions and of test_SystemParser for fail_invalid_aligned system for congruence with new parser scheme. Add of new fake profiles for the new genes introduced in the def.
Not functional yet in search_systems.get_best_hits: Added tests for cases where hits have the same score, then sort hits also according to i-evalue. Commented for now
Update to ignore tests files