diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000000000000000000000000000000000000..47529749db45031dbf7cb065121a5a48bcc63f10 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,21 @@ +## [1.7.0] - 2024-08-21 +### Changed +- Update tool `Integron_finder` to version `2.0.5`. +### Breaking Changes +- **Incompatibility with previous versions**: This update prevents the use of tool versions lower than `2.0.5`. Make sure you update the tool to version `2.0.5` or higher to continue using the project. + +## [1.6.1] - 2024-08-21 +### Added +- Completion of the Class & Subclass fields in the fam.tab file following the update of the AMRfinder database. +### Fixed +- Patch recurring error in dependency test function. +- Update of pandas deprecated uses + +## [1.6.0] - 2024-08-20 +### Fixed +- Removal of sequences from the Corynebacterium_diphtheriae database following their addition to the AMRfinder database. +- Reallocation of "parent_node_id" after deletion of some due to ARMfinder database update. + +## [1.5.0] - 2024-03-04 +### Formatting +- Formatting of the Coryne resistance database in amrfinder 3.12 format. \ No newline at end of file diff --git a/__main__.py b/__main__.py index 653aa8e430b525f6eda17efaa83834450f0a34d0..cc87dbe1fac6757f51654cf9b3f55b56973d0421 100644 --- a/__main__.py +++ b/__main__.py @@ -53,7 +53,7 @@ Usage: __authors__ = ("Melanie HENNART; Martin RETHORET-PASTY") __contact__ = ("martin.rethoret-pasty@pasteur.fr") -__version__ = "1.6.1" +__version__ = "1.7.0" __copyright__ = "copyleft" __date__ = "2024/03/04" @@ -149,12 +149,12 @@ def test_required_dependency(args): test_multiple_dependencies(diphtoscan_dependencies) if args.integron: - rc = test_unique_dependency("integron_finder") + rc = test_unique_dependency("Integron_finder") test_multiple_dependencies(integron_fender_dependencies) if rc == 0: args.integron = True else: - print('/!\\ Warning /!\\ : integron_finder missing in path! Integron analysis not carried out.') + print('/!\\ Warning /!\\ : Integron_finder missing in path! Integron analysis not carried out.') args.integron = False if args.tree: @@ -378,7 +378,7 @@ if __name__ == "__main__": ' --gbk --func-annot --mute '+ genome) os.system('find '+ args.outdir + "/Results_Integron_Finder_*/ " + '-empty -type d -delete') - files = pd.read_csv(args.outdir + "/Results_Integron_Finder_"+strain + "/" + strain+".summary",sep="\t", index_col=0, skiprows = 1) + files = pd.read_csv(args.outdir + "/Results_Integron_Finder_"+strain + "/" + strain+".summary",sep="\t", index_col=0, skiprows = 2) dict_genome.update(files[['CALIN','complete','In0']].sum().to_dict()) dict_results[strain] = dict_genome