diff --git a/__main__.py b/__main__.py index 653aa8e430b525f6eda17efaa83834450f0a34d0..b164949dc9f770291a8416beef27f6c242370a54 100644 --- a/__main__.py +++ b/__main__.py @@ -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