diff --git a/src/specimen/util/set_up.py b/src/specimen/util/set_up.py index 309e7de..3680300 100644 --- a/src/specimen/util/set_up.py +++ b/src/specimen/util/set_up.py @@ -380,7 +380,7 @@ def dict_recursive_check(dictA:dict, key:str=None, # @TEST def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict: - """Guide the user step by step throuh the creation of the configuration for a cmpb pipeline run + """Guide the user step by step through the creation of the configuration for a cmpb pipeline run (via commandline). Args: @@ -443,7 +443,7 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict: config['general']['save_all_models'] = False # run memote always y/n - run_memote = click.prompt('Do you want run memote after each step?', type=click.Choice(['y','n']), show_choices=True) + run_memote = click.prompt('Do you want to run memote after each step?', type=click.Choice(['y','n']), show_choices=True) match run_memote: case 'y': config['general']['memote_always_on'] = True @@ -451,7 +451,7 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict: config['general']['memote_always_on'] = False # run stats always y/n - models_stats = click.prompt('Do you want run memote after each step?', type=click.Choice(['y','n']), show_choices=True) + models_stats = click.prompt('Do you want to run memote after each step?', type=click.Choice(['y','n']), show_choices=True) match models_stats: case 'y': config['general']['stats_always_on'] = True @@ -462,7 +462,7 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict: refseq = click.prompt('If you want to run a gap analysis with KEGG or have a CarveMe model, please enter the path to your refseq gff file', type=click.Path(exists=True)) config['general']['refseq_organism_id'] = refseq - kegg_org_id = click.prompt('If you want to run a gap analysis with KEGG or have a CarveMe model, please enter the path to your refseq gff file', type=click.Path(exists=True)) + kegg_org_id = click.prompt('If you want to run a gap analysis with KEGG, please enter the KEGG organism ID', type=click.Path(exists=True)) config['general']['refseq_organism_id'] = kegg_org_id # part-specific @@ -476,7 +476,7 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict: if carveme == 'y': email = click.prompt('Enter an email address for the connection to NCBI Entrez', type=str) config['cm-polish']['email'] = email - labs = click.prompt('Do you have a lab strain?', type=click.Choice(['y','n']), show_choices=True) + labs = click.prompt('Do you have a strain without any database information?', type=click.Choice(['y','n']), show_choices=True) labs = True if labs == 'y' else False config['cm-polish']['is_lab_strain'] = labs if labs: @@ -507,7 +507,7 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict: Path3 = click.prompt('Enter path to protein FASTA file used as input for CarveMe', type=click.Path(exists=True)) config['gapfilling']['gap_fill_params']['biocyc_files'] = [Path0, Path1, Path2, Path3] - +# @TODO: Funktioniert das so? Bei den anderen yes-no-Fragen hast du noch alles auf True oder False gesetzt. # kegg pathways as groups kegg_pw_groups = click.prompt('Do you want to add KEGG pathways as groups to the model?', type=click.Choice(['y','n']), show_choices=True) config['kegg_pathway_groups'] = kegg_pw_groups @@ -525,6 +525,7 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict: case 'n': config['duplicates']['remove_unused_metabs'] = False +# @TODO: Ask for any biomass correction # BOF do_bofdat = click.prompt('Do you want do run BOFdat?', type=click.Choice(['y','n']), show_choices=True) match do_bofdat: @@ -534,7 +535,7 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict: config['BOF']['full_genome_sequence'] = full_genome_path dna_wf = click.prompt('Enter the DNA weight fraction of your organism', type=float) config['BOF']['dna_weight_fraction'] = dna_wf - wf = click.prompt('Enter the wight fraction of your organsim (enzyme/ion)', type=float) + wf = click.prompt('Enter the weight fraction of your organsim (enzyme/ion)', type=float) config['BOF']['weight_fraction'] = wf case 'n': config['BOF']['run_bofdat'] = False