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update config input #8
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@niinina
niinina committed Aug 22, 2024
1 parent 4ddec67 commit 91ebf0b
Showing 1 changed file with 76 additions and 37 deletions.
113 changes: 76 additions & 37 deletions src/specimen/util/set_up.py
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Original file line number Diff line number Diff line change
Expand Up @@ -421,7 +421,6 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict:
print('------------')
print('The following information is REQUIRED for the pipeline')
print('------------')
config['input']['annotated_genome'] = click.prompt('Enter the path to your annotated genome file', type=click.Path(exists=True))
config['input']['mediapath'] = click.prompt('Enter the path to a media configuration file for growth simulation', type=click.Path(exists=True))

# general options
Expand All @@ -437,7 +436,7 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict:
set_col = click.prompt('Do you want to use the default colour map YlGn for the visualisation?', type=click.Choice(['y','n']), show_choices=True)
match set_col:
case 'n':
colours = click.prompt('Enter your choosen colour scheme', type=str)
colours = click.prompt('Enter your chosen colour scheme', type=str)
config['general']['colours'] = colours
case 'y':
pass
Expand Down Expand Up @@ -467,11 +466,25 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict:
config['general']['stats_always_on'] = False

# some additional, sometimes required, sometimes optional files
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))
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())
config['general']['refseq_organism_id'] = refseq

kegg_org_id = click.prompt('If you want to run a gap analysis with KEGG, please enter the KEGG organism ID')
config['general']['kegg_organism_id'] = kegg_org_id

protein_fasta = click.prompt('If you want to use CarveMe or GeneGapFiller, please enter the path to your protein fasta file', type=click.Path())
config['general']['protein_fasta'] = protein_fasta

# tech resources
# --------------
email = click.prompt('Enter the e-mail that will be used for Entrez')
config['tech-resources']['email'] = email

set_threads = click.prompt('The default number of threads available for tools like DIAMOND is 2. Do you want to change that?', type=click.Choice(['y','n']), show_choices=True)
match set_threads:
case 'y':
threads = click.prompt('Enter the number of threads available for tools like DIAMOND', type=int)
config['tech-resources']['threads'] = threads

# part-specific
# -------------
Expand All @@ -480,54 +493,81 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict:
print('------------')

# CarveMe
carve = click.prompt('Do you want to build a model using CarveMe', type=click.Choice(['y','n']), show_choices=True)
carve = click.prompt('Do you want to build a model using CarveMe?', type=click.Choice(['y','n']), show_choices=True)
match carve:
case 'y':
config['carveme']['run_carve'] = True
prot_fa = click.prompt('Please enter the path to your protein fasta file', type=click.Path(exists=True))
config['carveme']['protein_fasta'] = prot_fa
if config['general']['protein_fasta'] is None:
protein_fasta = click.prompt('Enter the path to your protein fasta file', type=click.Path(exists=True))
config['general']['protein_fasta'] = protein_fasta
gram = click.prompt('Do you want to use a template specialized for gram-positive or gram-negative bacteria?', type=click.Choice(['grampos','gramneg','None']), show_choices=True)
config['carveme']['gram'] = gram
case 'n':
config['carveme']['run_carve'] = False
if config['input']['modelpath'] is None:
model = click.prompt('Please choose between an existing model or building a model with CarveMe. To run the CMPB workflow, you need a model.', type=click.Choice(['modelpath','CarveMe']), show_choices=True)
match model:
case 'modelpath':
modelpath = click.prompt('Enter the path to an existing model', type=click.Path(exists=True))
config['input']['modelpath'] = modelpath
case 'CarveMe':
carveme = click.prompt('Enter the path to a protein fasta file', type=click.Path(exists=True))
config['general']['protein_fasta'] = carveme

# model polish
carveme = click.prompt('Is your draft model CarveMe-based or will CarveMe be run?', type=click.Choice(['y','n']), show_choices=True)
carveme = click.prompt('Is your draft model CarveMe-based?', type=click.Choice(['y','n']), show_choices=True)
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 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:
prot_fa = click.prompt('Please enter the path to your protein fasta file', type=click.Path(exists=True))
config['cm-polish']['protein_fasta'] = prot_fa
else:
check_prot_fa = click.prompt('Do you want to/can provide the protein fasta?', type=click.Choice(['y','n']), show_choices=True)
if check_prot_fa == 'y':
prot_fa = click.prompt('Please enter the path to your protein fasta file', type=click.Path(exists=True))
config['cm-polish']['protein_fasta'] = prot_fa
else:
config['cm-polish']['protein_fasta'] = None


# gapfilling
gap_analysis = click.prompt('Do you want to run a gap analysis?', type=click.Choice(['y','n']), show_choices=True)

if gap_analysis == 'y':
db_to_compare = click.prompt('Available database information for the gapfilling', type=click.Choice(['KEGG','BioCyc','KEGG+BioCyc']), show_choices=True)
config['gapfilling']['gap_fill_params']['db_to_compare'] = db_to_compare

if 'KEGG' in db_to_compare:
pass
if 'BioCyc' in db_to_compare:
Path0 = click.prompt('Enter the path to your BioCyc TXT file containing a SmartTable with the columns \'Accession-2\' and \'Reaction of gene\'', type=click.Path(exists=True))
Path1 = click.prompt('Enter the path to your BioCyc TXT file containing a SmartTable with all reaction relevant information', type=click.Path(exists=True))
Path2 = click.prompt('Enter the path to your Biocyc TXT file containing a SmartTable with all metabolite relevant information', type=click.Path(exists=True))
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. -> Habs geändert, weil sonst steht in der config n und es wird trotzdem durchgeführt
idprefix = click.prompt('Enter a prefix to be used of IDs for the namespace do not exist')
config['gapfilling']['idprefix'] = idprefix
formula_check = click.prompt('Enter the parameter for checking the metabolite formula before adding them to the model', type=click.Choice(['none','strict','existence','wildcard']), show_choices=True)
config['gapfilling']['formula-check'] = formula_check
exclude_dna = click.prompt('Do you want to exlude reactions containing \'DNA\' in their name?', type=click.Choice(['y','n']), show_choices=True)
config['gapfilling']['exclude-dna'] = exclude_dna
exclude_rna = click.prompt('Do you want to exlude reactions containing \'RNA\' in their name?', type=click.Choice(['y','n']), show_choices=True)
config['gapfilling']['exclude-rna'] = exclude_rna

algorithm = click.prompt('Which algorithm do you want to use for gapfilling?', type=click.Choice(['KEGGapFiller','BioCycGapFiller','GeneGapFiller']), show_choices=True)
match algorithm:
case 'KEGGapFiller':
config['gapfilling']['KEGGapFiller'] = True

if config['general']['kegg_organism_id'] is None:
kegg_org_id = click.prompt('Enter the KEGG organism id')
config['general']['kegg_organism_id'] = kegg_org_id
case 'BioCycGapFiller':
config['gapfilling']['BioCycGapFiller'] = True

gene_table = click.prompt('Enter the path to a gene smart table from BioCyc', type=click.Path(exists=True))
config['gapfilling']['BioCycGapFiller parameters']['gene-table'] = gene_table
reacs_table = click.prompt('Enter the path to a reactions smart table from BioCyc', type=click.Path(exists=True))
config['gapfilling']['BioCycGapFiller parameters']['reacs-table'] = reacs_table
gff = click.prompt('Enter the path to a GFF file of the genome of the model', type=click.Path(exists=True))
config['gapfilling']['BioCycGapFiller parameters']['gff'] = gff
case 'GeneGapFiller':
config['gapfilling']['GeneGapFiller'] = True

gff = click.prompt('Enter the path to a GFF file of the genome of the model', type=click.Path(exists=True))
config['gapfilling']['GeneGapFiller parameters']['gff'] = gff
swissprot_dmnd = click.prompt('Enter the path to the SwissProt DIAMOND database file', type=click.Path(exists=True))
config['gapfilling']['GeneGapFiller parameters']['swissprot-dmnd'] = swissprot_dmnd
swissprot_mapping = click.prompt('Enter the path to the SwissProt mapping file', type=click.Path(exists=True))
config['gapfilling']['GeneGapFiller parameters']['swissprot-mapping'] = swissprot_mapping
check_NCBI = click.prompt('Do you want to enable checking NCBI accession numbers for EC numbers?', type=click.Choice(['y','n']), show_choices=True)
check_NCBI = True if check_NCBI == 'y' else False
config['gapfilling']['GeneGapFiller parameters']['check-NCBI'] = check_NCBI
sensitivity = click.prompt('Enter the sensitivity option for the DIAMOND run', type=click.Choice(['fast','mid-sensitive','sensitive','more-sensitive','very-sensitive','ultra-sensitive']), show_choices=True)
config['gapfilling']['GeneGapFiller parameters']['sensitivity'] = sensitivity
coverage = click.prompt('Enter the coverage for DIAMOND', type=float)
config['gapfilling']['GeneGapFiller parameters']['coverage'] = coverage
percentage_identity = click.prompt('Enter the percentage identity threshold value for accepting matches', type=float)
config['gapfilling']['GeneGapFiller parameters']['percentage identity'] = percentage_identity

# 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)
match kegg_pw_groups:
Expand All @@ -537,7 +577,6 @@ def save_cmpb_user_input(configpath:Union[str,None]=None) -> dict:
config['kegg_pathway_groups'] = False

# resolve duplicates

reac_dups = click.prompt('Do you want to check for and/or remove duplicate reactions?', type=click.Choice(['skip','check','remove']), show_choices=True)
config['duplicates']['reactions'] = reac_dups
meta_dups = click.prompt('Do you want to check for and/or remove duplicate metabolites?', type=click.Choice(['skip','check','remove']), show_choices=True)
Expand All @@ -559,7 +598,7 @@ 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 weight fraction of your organsim (enzyme/ion)', type=float)
wf = click.prompt('Enter the weight fraction of your organism (enzyme/ion)', type=float)
config['BOF']['weight_fraction'] = wf
case 'n':
config['BOF']['run_bofdat'] = False
Expand Down

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